[gmx-users] Re:request

[Kia Balali-Mood]

Hi Hadi,

It appears to me that you've not included (eg. #include "drg.itp) the molecule
specific topology in the *top file.

Also, (prob more for future reference) please note that the order you have your
molecules in your coordinate (*pdb or *gro) file should be the order they are
presented in your *top file.

cheers

Kia

> Message: 4
> Date: Mon, 4 Dec 2006 09:52:01 -0800 (PST)
> From: hadi behzadi <behzadihadi at yahoo.com>
> Subject: [gmx-users] request
> To: gmx-users at gromacs.org
> Message-ID: <278189.85222.qm at web53009.mail.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 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 dava at davapc1.bioch.dundee.ac.uk
>   ;       
>   ;       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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-- 
Kia Balali-Mood PhD, CBiol, MIBiol
Postdoctoral Research Associate, Department of Biochemistry, 
Oxford University, OX1 3QU, UK
sansom.biop.ox.ac.uk/kia/ , tel. +44 (0)1865 275 (380 or 275)