On 9/21/15 8:06 AM, Daniele Veclani wrote:
Dear Gromacs Useres
I'm trying to study a molecule in methanol (I have already studied this
molecule in water) with charmm27 force field.
I created the file .itp for methanol (solvent):
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
CR 6 12.0110 0.0 A 0.387541 0.230120
HCMM 1 1.0079 0.0 A 0.235197 0.092048
OR 8 15.9994 0.0 A 0.315378 0.636386
HOR 1 1.0079 0.0 A 0.040001 0.192464
[ pairtypes ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4
INTERACTIONS
CR CR 1 0.338541 0.041840
CR HCMM 1 0.286869 0.062059
CR OR 1 0.326960 0.163176
CR HOR 1 0.189271 0.089737
[ moleculetype ]
; Name nrexcl
SOL 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CR 1 SOL C 1 0.2800 12.0110
2 HCMM 1 SOL H 2 0.0000 1.0079
3 HCMM 1 SOL H1 3 0.0000 1.0079
4 HCMM 1 SOL H2 4 0.0000 1.0079
5 OR 1 SOL O 5 -0.6800 15.9994
6 HOR 1 SOL H3 6 0.4000 1.0079
[ bonds ]
; ai aj fu b0 kb, b0 kb
5 6 1 0.09720 469365.3 0.09720 469365.3
5 1 1 0.14180 303937.5 0.14180 303937.5
2 1 1 0.10930 287014.9 0.10930 287014.9
1 4 1 0.10930 287014.9 0.10930 287014.9
1 3 1 0.10930 287014.9 0.10930 287014.9
[ pairs ]
; ai aj fu
2 6 1
3 6 1
4 6 1
[ angles ]
; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
2 1 3 1 108.8360 310.74 108.8360 310.74
2 1 4 1 108.8360 310.74 108.8360 310.74
2 1 5 1 108.5770 470.32 108.5770 470.32
3 1 4 1 108.8360 310.74 108.8360 310.74
3 1 5 1 108.5770 470.32 108.5770 470.32
4 1 5 1 108.5770 470.32 108.5770 470.32
1 5 6 1 106.5030 477.55 106.5030 477.55
[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0 kphi mult
2 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1
2 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2
2 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3
3 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1
3 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2
3 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3
4 1 5 6 9 0.00 1.2468 1 0.00 1.2468 1
4 1 5 6 9 180.00 -0.5774 2 180.00 -0.5774 2
4 1 5 6 9 0.00 0.7238 3 0.00 0.7238 3
[ dihedrals ]
; ai aj ak al fu xi0 kxi xi0 kxi
1 2 5 4 2 0.00 0.0000 0.00 0.0000
1 2 5 3 2 0.00 0.0000 0.00 0.0000
#ifdef POSRES_LIGAND
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
5 1 1000 1000 1000
#endif
And I included this file in the topology file:
#include "charmm27.ff/forcefield.itp"
#include "charmm27.ff/nor-antib.itp"
#include "charmm27.ff/metanolo.itp"
[ system ]
; Name
nor
[ molecules ]
; Compound #mols
SOL 1000
nor-antib 1
when I run grompp i get this error:
Fatal error:
Syntax error - File metanolo.itp, line 7
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
What am I doing wrong?? (i use gromacs 5.0.4)
Please search the archive (I answer this question weekly) and/or visit the
GROMACS Error page, which discusses this situation/error specifically.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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