Hi all users
I constructed topology and gro (1.gro and 1.top) file for propane (
CH3CH2CH3) molecule from PRODRG server as follow:
1.go
PRODRG COORDS
3
1DRG CAB 1 -0.128 0.172 0.000
1DRG CAA 2 -0.128 0.019 0.000
1DRG CAC 3 0.017 -0.033 0.000
0.35530 0.35530 0.35530
1.top
;
;
; This file was generated by PRODRG version 061128.0522
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to [EMAIL PROTECTED]
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
;
;
[ moleculetype ]
; Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CAB 1 -0.012 15.0350
2 CH2 1 DRG CAA 1 0.024 14.0270
3 CH3 1 DRG CAC 1 -0.012 15.0350
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.153 334720.0 0.153 334720.0 ; CAB CAA
2 3 1 0.153 334720.0 0.153 334720.0 ; CAA CAC
[ pairs ]
; ai aj fu c0, c1, ...
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 111.0 460.2 111.0 460.2 ; CAB CAA CAC
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
Then, I construct 88 molecule of propane with editconf and genbox :
editconf f 1.gro -0 1.pdb d 0.3
genbox -cs 1.pdb -p 1.top -o 3.pdb -box 3 3 3
then I chaned the topology file by adding the following phrase in the end
of 1.top:
[ system ]
; Name DRG
[ molecules ]
; Compound #mols
DRG 88
When I want to performer the following commend :
grompp -v -f grompp.mdp -c b4em.pdb -p 1.top o
I encounter to this error :
Program grompp, VERSION 3.3
Source code file: topio.c, line: 385
Fatal error:
Invalid order for directive moleculetype, file ""1.top"", line 17
The line 17 is [ moleculetype ].
I request you all to give suggestion for this.
I will be very thankful to you.
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