mirror of
https://github.com/cp2k/cp2k.git
synced 2026-07-28 06:05:29 -04:00
bug fix for onfo for 5 and 6 membered rings.. introducing 2 specific regtests..
resetting loop.inp. svn-origin-rev: 5188
This commit is contained in:
Teodoro Laino
parent
f100c4362d
commit
bdfc9a5712
13 changed files with 619 additions and 18 deletions
|
|
@ -312,6 +312,10 @@ SUBROUTINE fist_force_control ( fist_env, virial, globenv, debug ,error)
|
|||
ENDIF
|
||||
|
||||
IF (iw>0) THEN
|
||||
WRITE(iw,'(1x,"BOND = ",f13.4,2x,"ANGLE = ",f13.4,2x,'//&
|
||||
'"DIHED = ",f13.4)')pot_bond, pot_bend,pot_torsion+pot_imptors
|
||||
WRITE(iw,'(1x,"1-4 VDW + 1-4 EEL (SHORT RANGE) = ",f13.4,2x,'//&
|
||||
'"UBRAD = ",f13.4)')pot_onef,pot_urey_bradley
|
||||
WRITE(iw,'(A)')" FIST:: CORRECTED BONDED ELECTROSTATIC FORCES + INTERNAL FORCES..."
|
||||
WRITE(iw,'(3f15.9)')((particle_set ( i ) % f ( j ),j=1,3), i = 1, SIZE(particle_set))
|
||||
END IF
|
||||
|
|
|
|||
|
|
@ -41,6 +41,8 @@ MODULE topology_psf
|
|||
USE topology_types, ONLY: atom_info_type,&
|
||||
connectivity_info_type,&
|
||||
topology_parameters_type
|
||||
USE topology_util, ONLY: reorder_structure,&
|
||||
atom_bond_list_type
|
||||
#include "cp_common_uses.h"
|
||||
|
||||
IMPLICIT NONE
|
||||
|
|
@ -157,12 +159,14 @@ CONTAINS
|
|||
CHARACTER(LEN=default_string_length) :: dummy_field, label
|
||||
INTEGER :: handle, i, iatom, ibond, index_now, iphi, itheta, iw, jatom, &
|
||||
natom, natom_prev, nbond, nbond_prev, nphi, nphi_prev, ntheta, &
|
||||
ntheta_prev
|
||||
ntheta_prev, nonfo, ionfo, nonfo_prev, stat, N
|
||||
LOGICAL :: failure, found
|
||||
TYPE(atom_info_type), POINTER :: atom_info
|
||||
TYPE(connectivity_info_type), POINTER :: conn_info
|
||||
TYPE(cp_logger_type), POINTER :: logger
|
||||
TYPE(cp_parser_type), POINTER :: parser
|
||||
TYPE(atom_bond_list_type), DIMENSION(:), POINTER :: ex_bond_list,&
|
||||
ex_bend_list
|
||||
|
||||
NULLIFY(parser, logger)
|
||||
logger => cp_error_get_logger(error)
|
||||
|
|
@ -310,15 +314,16 @@ CONTAINS
|
|||
!
|
||||
! PHI section
|
||||
!
|
||||
nphi_prev = 0
|
||||
IF(ASSOCIATED(conn_info%phi_a)) nphi_prev = SIZE(conn_info%phi_a)
|
||||
|
||||
nphi_prev = 0
|
||||
nonfo_prev = 0
|
||||
IF(ASSOCIATED(conn_info%phi_a)) nphi_prev = SIZE(conn_info%phi_a)
|
||||
IF(ASSOCIATED(conn_info%onfo_a)) nonfo_prev = SIZE(conn_info%onfo_a)
|
||||
IF(iw>0) WRITE(iw,'(T2,A)') 'PSF_INFO| Parsing the NPHI section'
|
||||
label = '!NPHI'
|
||||
CALL parser_search_string(parser,label,.TRUE.,found,begin_line=.TRUE.)
|
||||
IF ( .NOT. found ) THEN
|
||||
IF(iw>0) WRITE (iw,'(T2,A)') 'PSF_INFO| No NPHI section '
|
||||
nphi = 0
|
||||
nphi = 0
|
||||
ELSE
|
||||
CALL parser_get_object (parser,nphi)
|
||||
IF(iw>0) WRITE(iw,'(T2,A,I8)') 'PSF_INFO| NPHI = ',nphi
|
||||
|
|
@ -327,8 +332,8 @@ CONTAINS
|
|||
CALL reallocate(conn_info%phi_b,1,nphi_prev+nphi)
|
||||
CALL reallocate(conn_info%phi_c,1,nphi_prev+nphi)
|
||||
CALL reallocate(conn_info%phi_d,1,nphi_prev+nphi)
|
||||
CALL reallocate(conn_info%onfo_a,1,nphi_prev+nphi)
|
||||
CALL reallocate(conn_info%onfo_b,1,nphi_prev+nphi)
|
||||
CALL reallocate(conn_info%onfo_a,1,nonfo_prev+nphi)
|
||||
CALL reallocate(conn_info%onfo_b,1,nonfo_prev+nphi)
|
||||
!Read in the torsion info
|
||||
DO iphi=1,nphi,2
|
||||
CALL parser_get_next_line(parser,1,error=error)
|
||||
|
|
@ -346,9 +351,83 @@ CONTAINS
|
|||
END IF
|
||||
!
|
||||
! ONFO structure
|
||||
!
|
||||
!
|
||||
conn_info%onfo_a(:) = conn_info%phi_a(:)
|
||||
conn_info%onfo_b(:) = conn_info%phi_d(:)
|
||||
! Reorder bonds
|
||||
ALLOCATE(ex_bond_list(natom),stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
DO I=1,natom
|
||||
ALLOCATE(ex_bond_list(I)%bonds(0),stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
ENDDO
|
||||
N = 0
|
||||
IF(ASSOCIATED(conn_info%bond_a)) N = SIZE(conn_info%bond_a)
|
||||
CALL reorder_structure(ex_bond_list, conn_info%bond_a, conn_info%bond_b, N, error)
|
||||
! Reorder bends
|
||||
ALLOCATE(ex_bend_list(natom),stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
DO I=1,natom
|
||||
ALLOCATE(ex_bend_list(I)%bonds(0),stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
ENDDO
|
||||
N = 0
|
||||
IF(ASSOCIATED(conn_info%theta_a)) N = SIZE(conn_info%theta_a)
|
||||
CALL reorder_structure(ex_bend_list, conn_info%theta_a, conn_info%theta_c, N, error)
|
||||
nonfo = 0
|
||||
DO ionfo=1, nphi
|
||||
! Check if the torsion is not shared between angles or bonds
|
||||
IF ( ANY(ex_bond_list(conn_info%onfo_a(ionfo))%bonds==conn_info%onfo_b(ionfo)).OR.&
|
||||
ANY(ex_bend_list(conn_info%onfo_a(ionfo))%bonds==conn_info%onfo_b(ionfo))) CYCLE
|
||||
nonfo = nonfo + 1
|
||||
conn_info%onfo_a(nonfo) = conn_info%onfo_a(ionfo)
|
||||
conn_info%onfo_b(nonfo) = conn_info%onfo_b(ionfo)
|
||||
END DO
|
||||
! deallocate bends
|
||||
DO I=1,natom
|
||||
DEALLOCATE(ex_bend_list(I)%bonds,stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
ENDDO
|
||||
DEALLOCATE(ex_bend_list,stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
! deallocate bonds
|
||||
DO I=1,natom
|
||||
DEALLOCATE(ex_bond_list(I)%bonds,stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
ENDDO
|
||||
DEALLOCATE(ex_bond_list,stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
! Get unique onfo
|
||||
ALLOCATE(ex_bond_list(natom),stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
DO I=1,natom
|
||||
ALLOCATE(ex_bond_list(I)%bonds(0),stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
ENDDO
|
||||
N = 0
|
||||
IF(ASSOCIATED(conn_info%onfo_a)) N = nonfo_prev+nonfo
|
||||
CALL reorder_structure(ex_bond_list, conn_info%onfo_a, conn_info%onfo_b, N, error)
|
||||
nonfo = 0
|
||||
DO I=1,natom
|
||||
DO ionfo = 1, SIZE(ex_bond_list(I)%bonds)
|
||||
IF (COUNT(ex_bond_list(I)%bonds==ex_bond_list(I)%bonds(ionfo))/=1) THEN
|
||||
ex_bond_list(I)%bonds(ionfo) = 0
|
||||
ELSE
|
||||
IF (ex_bond_list(I)%bonds(ionfo)<=I) CYCLE
|
||||
nonfo = nonfo + 1
|
||||
conn_info%onfo_a(nonfo_prev+nonfo) = I
|
||||
conn_info%onfo_b(nonfo_prev+nonfo) = ex_bond_list(I)%bonds(ionfo)
|
||||
END IF
|
||||
END DO
|
||||
END DO
|
||||
CALL reallocate(conn_info%onfo_a,1,nonfo_prev+nonfo)
|
||||
CALL reallocate(conn_info%onfo_b,1,nonfo_prev+nonfo)
|
||||
DO I=1,natom
|
||||
DEALLOCATE(ex_bond_list(I)%bonds,stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
ENDDO
|
||||
DEALLOCATE(ex_bond_list,stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
!
|
||||
! IMPHI section
|
||||
!
|
||||
|
|
|
|||
|
|
@ -107,7 +107,9 @@ MODULE topology_util
|
|||
topology_generate_onfo,&
|
||||
topology_generate_ub,&
|
||||
topology_molecules_check,&
|
||||
check_subsys_element
|
||||
check_subsys_element,&
|
||||
reorder_structure,&
|
||||
atom_bond_list_type
|
||||
|
||||
!!*****
|
||||
!******************************************************************************
|
||||
|
|
@ -2393,7 +2395,7 @@ CONTAINS
|
|||
INTEGER :: counter, first, first_atom, handle, i, iatom, ibend, ibond, &
|
||||
ikind, imol_now, imolecule, itorsion, iw, j, k, handle3, kk, n,&
|
||||
last, last_atom, natom, nbend, nbond, ntorsion, position, stat, handle2
|
||||
INTEGER :: dim1, dim2, dim3
|
||||
INTEGER :: dim0, dim1, dim2, dim3
|
||||
INTEGER, DIMENSION(:), POINTER :: atomkind, iatomlist, first_mol, kind_of, &
|
||||
last_mol, list, list2, wlist, molecule_list, natom_of_kind
|
||||
LOGICAL :: failure, found, my_qmmm
|
||||
|
|
@ -2662,23 +2664,27 @@ CONTAINS
|
|||
CALL reorder_structure(ex_torsion_list, conn_info%phi_a, conn_info%phi_d, N, error)
|
||||
!
|
||||
DO iatom = 1, SIZE(particle_set)
|
||||
dim1 = 1 ! always exclude itself..
|
||||
dim0 = 1 ! always exclude itself
|
||||
dim1 = 0
|
||||
dim2 = 0
|
||||
dim3 = 0
|
||||
IF (topology%exclude_vdw==do_skip_vdw_12 .OR. &
|
||||
topology%exclude_vdw==do_skip_vdw_13 .OR. &
|
||||
topology%exclude_vdw==do_skip_vdw_14) dim1 = dim1 + SIZE(ex_bond_list(iatom)%bonds)
|
||||
topology%exclude_vdw==do_skip_vdw_14) dim1 = SIZE(ex_bond_list(iatom)%bonds)
|
||||
dim1 = dim0 + dim1
|
||||
IF (topology%exclude_vdw==do_skip_vdw_13 .OR. &
|
||||
topology%exclude_vdw==do_skip_vdw_14) dim2 = dim1 + SIZE(ex_bend_list(iatom)%bonds)
|
||||
IF (topology%exclude_vdw==do_skip_vdw_14) dim3 = dim2 + SIZE(ex_torsion_list(iatom)%bonds)
|
||||
topology%exclude_vdw==do_skip_vdw_14) dim2 = SIZE(ex_bend_list(iatom)%bonds)
|
||||
dim2 = dim1 + dim2
|
||||
IF (topology%exclude_vdw==do_skip_vdw_14) dim3 = SIZE(ex_torsion_list(iatom)%bonds)
|
||||
dim3 = dim2 + dim3
|
||||
IF (dim3 /= 0) THEN
|
||||
NULLIFY(list, wlist)
|
||||
ALLOCATE(wlist(dim3),stat=stat)
|
||||
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
|
||||
wlist( 1: 1) = iatom
|
||||
wlist( 2:dim1) = ex_bond_list(iatom)%bonds
|
||||
wlist(dim1+1:dim2) = ex_bend_list(iatom)%bonds
|
||||
wlist(dim2+1:dim3) = ex_torsion_list(iatom)%bonds
|
||||
wlist( dim0:dim0) = iatom
|
||||
IF (dim1>dim0) wlist(dim0+1:dim1) = ex_bond_list(iatom)%bonds
|
||||
IF (dim2>dim1) wlist(dim1+1:dim2) = ex_bend_list(iatom)%bonds
|
||||
IF (dim3>dim2) wlist(dim2+1:dim3) = ex_torsion_list(iatom)%bonds
|
||||
! Get a unique list
|
||||
DO i = 1, SIZE(wlist)-1
|
||||
IF (wlist(i)==0)CYCLE
|
||||
|
|
|
|||
|
|
@ -88,3 +88,5 @@ ethene_colv2_npt.inp 2
|
|||
H2O-32_SPME_fp.inp 2
|
||||
# testing loops in topology
|
||||
loop.inp 2
|
||||
pentadiene.inp 2
|
||||
cyhex.inp 2
|
||||
|
|
|
|||
|
|
@ -168,3 +168,5 @@ water_3_dist.inp
|
|||
water_hbonds_dist.inp
|
||||
#new linear scaling setup algorithms.. numerics for loop.inp (10^-12)
|
||||
loop.inp
|
||||
#bug fix for onfo
|
||||
loop.inp
|
||||
|
|
|
|||
51
tests/Fist/regtest/cyhex.inp
Normal file
51
tests/Fist/regtest/cyhex.inp
Normal file
|
|
@ -0,0 +1,51 @@
|
|||
|
||||
&FORCE_EVAL
|
||||
&MM
|
||||
&FORCEFIELD
|
||||
parmfile ../sample_pot/cyhex.pot
|
||||
parmtype CHM
|
||||
&END FORCEFIELD
|
||||
&POISSON
|
||||
&EWALD
|
||||
EWALD_TYPE ewald
|
||||
ALPHA .36
|
||||
GMAX 29
|
||||
&END EWALD
|
||||
&END POISSON
|
||||
&END MM
|
||||
&SUBSYS
|
||||
&CELL
|
||||
ABC 50.0 50.0 50.0
|
||||
UNIT ANGSTROM
|
||||
&END CELL
|
||||
&TOPOLOGY
|
||||
CHARGE_BETA
|
||||
CONN_FILE cyhex.psf
|
||||
CONNECTIVITY PSF
|
||||
COORD_FILE_NAME ../sample_pdb/cyhex.pdb
|
||||
COORDINATE PDB
|
||||
EXCLUDE_EI 1-3
|
||||
EXCLUDE_VDW 1-3
|
||||
&END TOPOLOGY
|
||||
&PRINT
|
||||
&TOPOLOGY_INFO
|
||||
UTIL_INFO
|
||||
&END
|
||||
&END
|
||||
&END SUBSYS
|
||||
&END FORCE_EVAL
|
||||
&GLOBAL
|
||||
FFTLIB FFTSG
|
||||
PRINT_LEVEL DEBUG
|
||||
PROGRAM FIST
|
||||
PROJECT mol
|
||||
RUN_TYPE md
|
||||
&END GLOBAL
|
||||
&MOTION
|
||||
&MD
|
||||
ENSEMBLE NVE
|
||||
STEPS 10
|
||||
TIMESTEP 2.5
|
||||
TEMPERATURE 0.0
|
||||
&END MD
|
||||
&END MOTION
|
||||
86
tests/Fist/regtest/cyhex.psf
Normal file
86
tests/Fist/regtest/cyhex.psf
Normal file
|
|
@ -0,0 +1,86 @@
|
|||
PSF
|
||||
|
||||
1 !NTITLE
|
||||
Conversion from AMBER PARMTOP ::MOL
|
||||
|
||||
17 !NATOM
|
||||
1 MOL01 1 MOL O1 o -0.54137 16.00000 0
|
||||
2 MOL01 1 MOL C2 c 0.45857 12.01000 0
|
||||
3 MOL01 1 MOL C1 c31 0.00588 12.01000 0
|
||||
4 MOL01 1 MOL H9 hc1 0.01000 1.00800 0
|
||||
5 MOL01 1 MOL H10 hc1 0.01000 1.00800 0
|
||||
6 MOL01 1 MOL C6 c32 0.01298 12.01000 0
|
||||
7 MOL01 1 MOL H7 hc2 0.00415 1.00800 0
|
||||
8 MOL01 1 MOL H8 hc2 0.00415 1.00800 0
|
||||
9 MOL01 1 MOL C5 c33 -0.00517 12.01000 0
|
||||
10 MOL01 1 MOL H5 hc3 -0.00317 1.00800 0
|
||||
11 MOL01 1 MOL H6 hc3 -0.00317 1.00800 0
|
||||
12 MOL01 1 MOL C4 c32 0.01298 12.01000 0
|
||||
13 MOL01 1 MOL H3 hc2 0.00415 1.00800 0
|
||||
14 MOL01 1 MOL H4 hc2 0.00415 1.00800 0
|
||||
15 MOL01 1 MOL C3 c31 0.00588 12.01000 0
|
||||
16 MOL01 1 MOL H1 hc1 0.01000 1.00800 0
|
||||
17 MOL01 1 MOL H2 hc1 0.01000 1.00800 0
|
||||
|
||||
17 !NBOND
|
||||
3 4 3 5 6 7 6 8
|
||||
9 10 9 11 12 13 12 14
|
||||
15 16 15 17 1 2 2 3
|
||||
2 15 3 6 6 9 9 12
|
||||
12 15
|
||||
|
||||
33 !NTHETA
|
||||
2 3 4 2 3 5 2 15 16
|
||||
2 15 17 3 6 7 3 6 8
|
||||
4 3 5 4 3 6 5 3 6
|
||||
6 9 10 6 9 11 7 6 8
|
||||
7 6 9 8 6 9 9 12 13
|
||||
9 12 14 10 9 11 10 9 12
|
||||
11 9 12 12 15 16 12 15 17
|
||||
13 12 14 13 12 15 14 12 15
|
||||
16 15 17 1 2 3 1 2 15
|
||||
2 3 6 2 15 12 3 2 15
|
||||
3 6 9 6 9 12 9 12 15
|
||||
|
||||
59 !NPHI
|
||||
1 2 3 4 1 2 3 4
|
||||
1 2 3 5 1 2 3 5
|
||||
1 2 15 16 1 2 15 16
|
||||
1 2 15 16 1 2 15 17
|
||||
1 2 15 17 1 2 15 17
|
||||
2 3 6 7 2 3 6 8
|
||||
2 15 12 13 2 15 12 14
|
||||
3 2 15 16 3 2 15 17
|
||||
3 6 9 10 3 6 9 11
|
||||
4 3 2 15 4 3 6 7
|
||||
4 3 6 8 4 3 6 9
|
||||
5 3 2 15 5 3 6 7
|
||||
5 3 6 8 5 3 6 9
|
||||
6 9 12 13 6 9 12 14
|
||||
7 6 9 10 7 6 9 11
|
||||
7 6 9 12 8 6 9 10
|
||||
8 6 9 11 8 6 9 12
|
||||
9 12 15 16 9 12 15 17
|
||||
10 9 12 13 10 9 12 14
|
||||
10 9 12 15 11 9 12 13
|
||||
11 9 12 14 11 9 12 15
|
||||
13 12 15 16 13 12 15 17
|
||||
14 12 15 16 14 12 15 17
|
||||
1 2 3 6 1 2 15 12
|
||||
2 3 6 9 2 15 12 9
|
||||
3 2 15 12 3 6 9 12
|
||||
3 6 9 12 3 6 9 12
|
||||
6 3 2 15 6 9 12 15
|
||||
6 9 12 15 6 9 12 15
|
||||
1 2 15 3
|
||||
|
||||
0 !NIMPHI
|
||||
|
||||
0 !NDON
|
||||
|
||||
0 !NACC
|
||||
|
||||
0 !NNB
|
||||
|
||||
0 !NGRP
|
||||
|
||||
51
tests/Fist/regtest/pentadiene.inp
Normal file
51
tests/Fist/regtest/pentadiene.inp
Normal file
|
|
@ -0,0 +1,51 @@
|
|||
|
||||
&FORCE_EVAL
|
||||
&MM
|
||||
&FORCEFIELD
|
||||
parmfile ../sample_pot/pentadiene.pot
|
||||
parmtype CHM
|
||||
&END FORCEFIELD
|
||||
&POISSON
|
||||
&EWALD
|
||||
EWALD_TYPE ewald
|
||||
ALPHA .36
|
||||
GMAX 29
|
||||
&END EWALD
|
||||
&END POISSON
|
||||
&END MM
|
||||
&SUBSYS
|
||||
&CELL
|
||||
ABC 50.0 50.0 50.0
|
||||
UNIT ANGSTROM
|
||||
&END CELL
|
||||
&TOPOLOGY
|
||||
CHARGE_BETA
|
||||
CONN_FILE pentadiene.psf
|
||||
CONNECTIVITY PSF
|
||||
COORD_FILE_NAME ../sample_pdb/pentadiene.pdb
|
||||
COORDINATE PDB
|
||||
EXCLUDE_EI 1-3
|
||||
EXCLUDE_VDW 1-3
|
||||
&END TOPOLOGY
|
||||
&PRINT
|
||||
&TOPOLOGY_INFO
|
||||
UTIL_INFO
|
||||
&END
|
||||
&END
|
||||
&END SUBSYS
|
||||
&END FORCE_EVAL
|
||||
&GLOBAL
|
||||
FFTLIB FFTSG
|
||||
PRINT_LEVEL DEBUG
|
||||
PROGRAM FIST
|
||||
PROJECT mol
|
||||
RUN_TYPE md
|
||||
&END GLOBAL
|
||||
&MOTION
|
||||
&MD
|
||||
ENSEMBLE NVE
|
||||
STEPS 10
|
||||
TIMESTEP 2.5
|
||||
TEMPERATURE 0.0
|
||||
&END MD
|
||||
&END MOTION
|
||||
55
tests/Fist/regtest/pentadiene.psf
Normal file
55
tests/Fist/regtest/pentadiene.psf
Normal file
|
|
@ -0,0 +1,55 @@
|
|||
PSF
|
||||
|
||||
1 !NTITLE
|
||||
Conversion from AMBER PARMTOP ::MOL
|
||||
|
||||
11 !NATOM
|
||||
1 MOL01 1 MOL C1 c2 -0.23818 12.01000 0
|
||||
2 MOL01 1 MOL H2 ha1 0.13221 1.00800 0
|
||||
3 MOL01 1 MOL C2 c3 0.08869 12.01000 0
|
||||
4 MOL01 1 MOL H5 hc 0.05151 1.00800 0
|
||||
5 MOL01 1 MOL H6 hc 0.05151 1.00800 0
|
||||
6 MOL01 1 MOL C3 c2 -0.23818 12.01000 0
|
||||
7 MOL01 1 MOL H1 ha1 0.13221 1.00800 0
|
||||
8 MOL01 1 MOL C4 ce -0.12914 12.01000 0
|
||||
9 MOL01 1 MOL H4 ha2 0.13926 1.00800 0
|
||||
10 MOL01 1 MOL C5 ce -0.12914 12.01000 0
|
||||
11 MOL01 1 MOL H3 ha2 0.13926 1.00800 0
|
||||
|
||||
11 !NBOND
|
||||
1 2 3 4 3 5 6 7
|
||||
8 9 10 11 1 3 1 10
|
||||
3 6 6 8 8 10
|
||||
|
||||
18 !NTHETA
|
||||
1 3 4 1 3 5 1 10 11
|
||||
2 1 3 2 1 10 3 6 7
|
||||
4 3 5 4 3 6 5 3 6
|
||||
6 8 9 7 6 8 8 10 11
|
||||
9 8 10 1 3 6 1 10 8
|
||||
3 1 10 3 6 8 6 8 10
|
||||
|
||||
24 !NPHI
|
||||
1 3 6 7 1 10 8 9
|
||||
2 1 3 4 2 1 3 5
|
||||
2 1 3 6 2 1 10 8
|
||||
2 1 10 11 3 1 10 11
|
||||
3 6 8 9 10 1 3 4
|
||||
4 3 6 7 4 3 6 8
|
||||
10 1 3 5 5 3 6 7
|
||||
5 3 6 8 6 8 10 11
|
||||
7 6 8 9 7 6 8 10
|
||||
9 8 10 11 1 3 6 8
|
||||
1 10 8 6 3 1 10 8
|
||||
3 6 8 10 10 1 3 6
|
||||
|
||||
0 !NIMPHI
|
||||
|
||||
0 !NDON
|
||||
|
||||
0 !NACC
|
||||
|
||||
0 !NNB
|
||||
|
||||
0 !NGRP
|
||||
|
||||
20
tests/Fist/sample_pdb/cyhex.pdb
Normal file
20
tests/Fist/sample_pdb/cyhex.pdb
Normal file
|
|
@ -0,0 +1,20 @@
|
|||
REMARK MOL
|
||||
ATOM 1 O1 MOL 1 3.537 1.423 0.000
|
||||
ATOM 2 C2 MOL 1 2.363 1.421 0.384
|
||||
ATOM 3 C1 MOL 1 1.612 0.145 0.651
|
||||
ATOM 4 H9 MOL 1 1.539 0.022 1.765
|
||||
ATOM 5 H10 MOL 1 2.192 -0.728 0.250
|
||||
ATOM 6 C6 MOL 1 0.228 0.168 0.042
|
||||
ATOM 7 H7 MOL 1 -0.337 -0.742 0.377
|
||||
ATOM 8 H8 MOL 1 0.310 0.118 -1.076
|
||||
ATOM 9 C5 MOL 1 -0.536 1.415 0.436
|
||||
ATOM 10 H5 MOL 1 -0.710 1.416 1.544
|
||||
ATOM 11 H6 MOL 1 -1.540 1.413 -0.064
|
||||
ATOM 12 C4 MOL 1 0.223 2.666 0.041
|
||||
ATOM 13 H3 MOL 1 -0.344 3.573 0.376
|
||||
ATOM 14 H4 MOL 1 0.307 2.716 -1.077
|
||||
ATOM 15 C3 MOL 1 1.609 2.693 0.651
|
||||
ATOM 16 H1 MOL 1 1.534 2.815 1.765
|
||||
ATOM 17 H2 MOL 1 2.186 3.567 0.251
|
||||
TER
|
||||
END
|
||||
14
tests/Fist/sample_pdb/pentadiene.pdb
Normal file
14
tests/Fist/sample_pdb/pentadiene.pdb
Normal file
|
|
@ -0,0 +1,14 @@
|
|||
REMARK MOL
|
||||
ATOM 1 C1 MOL 1 3.533 1.428 0.000
|
||||
ATOM 2 H2 MOL 1 3.855 0.389 0.000
|
||||
ATOM 3 C2 MOL 1 4.495 2.604 0.000
|
||||
ATOM 4 H5 MOL 1 5.125 2.605 -0.892
|
||||
ATOM 5 H6 MOL 1 5.125 2.605 0.893
|
||||
ATOM 6 C3 MOL 1 3.530 3.777 0.000
|
||||
ATOM 7 H1 MOL 1 3.849 4.817 0.000
|
||||
ATOM 8 C4 MOL 1 2.274 3.320 0.000
|
||||
ATOM 9 H4 MOL 1 1.354 3.905 0.000
|
||||
ATOM 10 C5 MOL 1 2.276 1.882 0.000
|
||||
ATOM 11 H3 MOL 1 1.358 1.294 0.000
|
||||
TER
|
||||
END
|
||||
123
tests/Fist/sample_pot/cyhex.pot
Normal file
123
tests/Fist/sample_pot/cyhex.pot
Normal file
|
|
@ -0,0 +1,123 @@
|
|||
*>>>>>>> AMBER FF Converted into CHARMM FF style <<<<<<<
|
||||
*>>>>>>> Generated on :: 20060524 214647.502 +0200 by :: teo <<<<<<<
|
||||
*>>>>>>> pcihpc07 <<<<<<<
|
||||
*>>>>>>> Leap Title :: MOL <<<<<<<
|
||||
*>>>>>>> Send all comments related to the FFs conversion to <<<<<<<
|
||||
*>>>>>>> teodoro.laino@gmail.com <<<<<<<
|
||||
|
||||
BONDS
|
||||
!
|
||||
!V(bond) = Kb(b - b0)**2
|
||||
!
|
||||
!Kb: kcal/mole/A**2
|
||||
!b0: A
|
||||
!
|
||||
!atom type Kb b0
|
||||
!
|
||||
c31 hc1 337.300000000 1.092000000
|
||||
c32 hc2 337.300000000 1.092000000
|
||||
c33 hc3 337.300000000 1.092000000
|
||||
o c 648.000000000 1.214000000
|
||||
c c31 328.300000000 1.508000000
|
||||
c31 c32 303.100000000 1.535000000
|
||||
c32 c33 303.100000000 1.535000000
|
||||
|
||||
ANGLES
|
||||
!
|
||||
!V(angle) = Ktheta(Theta - Theta0)**2
|
||||
!
|
||||
!V(Urey-Bradley) = Kub(S - S0)**2
|
||||
!
|
||||
!Ktheta: kcal/mole/rad**2
|
||||
!Theta0: degrees
|
||||
!Kub: kcal/mole/A**2 (Urey-Bradley)
|
||||
!S0: A
|
||||
!
|
||||
!atom types Ktheta Theta0 Kub S0
|
||||
!
|
||||
c c31 hc1 47.200000000 109.680046777
|
||||
c31 c32 hc2 46.400000000 110.050047451
|
||||
hc1 c31 hc1 39.400000000 108.350046723
|
||||
hc1 c31 c32 46.400000000 110.050047451
|
||||
c32 c33 hc3 46.400000000 110.050047451
|
||||
hc2 c32 hc2 39.400000000 108.350046723
|
||||
hc2 c32 c33 46.400000000 110.050047451
|
||||
hc3 c33 hc3 39.400000000 108.350046723
|
||||
o c c31 68.000000000 123.110052590
|
||||
c c31 c32 63.800000000 110.530047428
|
||||
c31 c c31 62.800000000 116.050050023
|
||||
c31 c32 c33 63.200000000 110.630047471
|
||||
c32 c33 c32 63.200000000 110.630047471
|
||||
|
||||
DIHEDRALS
|
||||
!
|
||||
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
|
||||
!
|
||||
!Kchi: kcal/mole
|
||||
!n: multiplicity
|
||||
!delta: degrees
|
||||
!
|
||||
!atom types Kchi n delta
|
||||
!
|
||||
o c c31 hc1 0.800000000 1 0.000000000
|
||||
o c c31 hc1 0.080000000 3 180.000077144
|
||||
o c c31 hc1 0.000000000 2 180.000077144
|
||||
c c31 c32 hc2 0.155555556 3 0.000000000
|
||||
c31 c c31 hc1 0.000000000 2 180.000077144
|
||||
c31 c32 c33 hc3 0.160000000 3 0.000000000
|
||||
hc1 c31 c32 hc2 0.150000000 3 0.000000000
|
||||
hc1 c31 c32 c33 0.160000000 3 0.000000000
|
||||
c32 c33 c32 hc2 0.160000000 3 0.000000000
|
||||
hc2 c32 c33 hc3 0.150000000 3 0.000000000
|
||||
o c c31 c32 0.000000000 2 180.000077144
|
||||
c c31 c32 c33 0.155555556 3 0.000000000
|
||||
c31 c c31 c32 0.000000000 2 180.000077144
|
||||
c31 c32 c33 c32 0.200000000 1 180.000077144
|
||||
c31 c32 c33 c32 0.250000000 2 180.000077144
|
||||
c31 c32 c33 c32 0.180000000 3 0.000000000
|
||||
o c c31 c31 10.500000000 2 180.000077144
|
||||
|
||||
IMPROPER
|
||||
!
|
||||
!V(improper) = Kpsi(psi - psi0)**2
|
||||
!
|
||||
!Kpsi: kcal/mole/rad**2
|
||||
!psi0: degrees
|
||||
!note that the second column of numbers (0) is ignored
|
||||
!
|
||||
!atom types Kpsi psi0
|
||||
!
|
||||
|
||||
NONBONDED
|
||||
!
|
||||
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
|
||||
!
|
||||
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
|
||||
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
|
||||
!
|
||||
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
|
||||
!
|
||||
o 0.000000000 0.210000000 1.661200000
|
||||
c 0.000000000 0.086000000 1.908000000
|
||||
c31 0.000000000 0.109400000 1.908000000
|
||||
hc1 0.000000000 0.015700000 1.487000000
|
||||
c32 0.000000000 0.109400000 1.908000000
|
||||
hc2 0.000000000 0.015700000 1.487000000
|
||||
c33 0.000000000 0.109400000 1.908000000
|
||||
hc3 0.000000000 0.015700000 1.487000000
|
||||
|
||||
END
|
||||
|
||||
!
|
||||
! This Section can be cutted & pasted into the Fist input file..
|
||||
!
|
||||
CHARGES
|
||||
o -0.541370000
|
||||
c 0.458570000
|
||||
c31 0.005880000
|
||||
hc1 0.010000000
|
||||
c32 0.012980000
|
||||
hc2 0.004150000
|
||||
c33 -0.005170000
|
||||
hc3 -0.003170000
|
||||
END CHARGES
|
||||
108
tests/Fist/sample_pot/pentadiene.pot
Normal file
108
tests/Fist/sample_pot/pentadiene.pot
Normal file
|
|
@ -0,0 +1,108 @@
|
|||
*>>>>>>> AMBER FF Converted into CHARMM FF style <<<<<<<
|
||||
*>>>>>>> Generated on :: 20060524 153444.174 +0200 by :: teo <<<<<<<
|
||||
*>>>>>>> pcihpc07 <<<<<<<
|
||||
*>>>>>>> Leap Title :: MOL <<<<<<<
|
||||
*>>>>>>> Send all comments related to the FFs conversion to <<<<<<<
|
||||
*>>>>>>> teodoro.laino@gmail.com <<<<<<<
|
||||
|
||||
BONDS
|
||||
!
|
||||
!V(bond) = Kb(b - b0)**2
|
||||
!
|
||||
!Kb: kcal/mole/A**2
|
||||
!b0: A
|
||||
!
|
||||
!atom type Kb b0
|
||||
!
|
||||
c2 ha1 344.300000000 1.087000000
|
||||
c3 hc 337.300000000 1.092000000
|
||||
ce ha2 341.500000000 1.089000000
|
||||
c2 c3 328.300000000 1.508000000
|
||||
c2 ce 560.500000000 1.339000000
|
||||
ce ce 390.500000000 1.451000000
|
||||
|
||||
ANGLES
|
||||
!
|
||||
!V(angle) = Ktheta(Theta - Theta0)**2
|
||||
!
|
||||
!V(Urey-Bradley) = Kub(S - S0)**2
|
||||
!
|
||||
!Ktheta: kcal/mole/rad**2
|
||||
!Theta0: degrees
|
||||
!Kub: kcal/mole/A**2 (Urey-Bradley)
|
||||
!S0: A
|
||||
!
|
||||
!atom types Ktheta Theta0 Kub S0
|
||||
!
|
||||
c2 c3 hc 47.000000000 110.490047525
|
||||
c2 ce ha2 49.600000000 121.100051901
|
||||
ha1 c2 c3 45.700000000 117.300050272
|
||||
ha1 c2 ce 49.600000000 121.190052111
|
||||
hc c3 hc 39.400000000 108.350046723
|
||||
ce ce ha2 47.500000000 115.900049672
|
||||
c2 c3 c2 64.600000000 109.710046847
|
||||
c2 ce ce 65.700000000 123.080052520
|
||||
c3 c2 ce 65.700000000 117.400050315
|
||||
|
||||
DIHEDRALS
|
||||
!
|
||||
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
|
||||
!
|
||||
!Kchi: kcal/mole
|
||||
!n: multiplicity
|
||||
!delta: degrees
|
||||
!
|
||||
!atom types Kchi n delta
|
||||
!
|
||||
c2 c3 c2 ha1 0.000000000 2 0.000000000
|
||||
c2 ce ce ha2 1.000000000 2 180.000077144
|
||||
ha1 c2 c3 hc 0.000000000 2 0.000000000
|
||||
ha1 c2 ce ce 6.650000000 2 180.000077144
|
||||
ha1 c2 ce ha2 6.650000000 2 180.000077144
|
||||
c3 c2 ce ha2 6.650000000 2 180.000077144
|
||||
ce c2 c3 hc 0.000000000 2 0.000000000
|
||||
ha2 ce ce ha2 1.000000000 2 180.000077144
|
||||
c2 c3 c2 ce 0.000000000 2 0.000000000
|
||||
c2 ce ce c2 1.000000000 2 180.000077144
|
||||
c3 c2 ce ce 6.650000000 2 180.000077144
|
||||
|
||||
IMPROPER
|
||||
!
|
||||
!V(improper) = Kpsi(psi - psi0)**2
|
||||
!
|
||||
!Kpsi: kcal/mole/rad**2
|
||||
!psi0: degrees
|
||||
!note that the second column of numbers (0) is ignored
|
||||
!
|
||||
!atom types Kpsi psi0
|
||||
!
|
||||
|
||||
NONBONDED
|
||||
!
|
||||
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
|
||||
!
|
||||
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
|
||||
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
|
||||
!
|
||||
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
|
||||
!
|
||||
c2 0.000000000 0.086000000 1.908000000
|
||||
ha1 0.000000000 0.015000000 1.459000000
|
||||
c3 0.000000000 0.109400000 1.908000000
|
||||
hc 0.000000000 0.015700000 1.487000000
|
||||
ce 0.000000000 0.086000000 1.908000000
|
||||
ha2 0.000000000 0.015000000 1.459000000
|
||||
|
||||
END
|
||||
|
||||
!
|
||||
! This Section can be cutted & pasted into the Fist input file..
|
||||
!
|
||||
CHARGES
|
||||
c2 -0.238180000
|
||||
ha1 0.132210000
|
||||
c3 0.088690000
|
||||
hc 0.051510000
|
||||
ce -0.129140000
|
||||
ha2 0.139260000
|
||||
END CHARGES
|
||||
Loading…
Add table
Add a link
Reference in a new issue