Fw: Re: [gmx-users] Methanol SOL :Number of solvent molecules = 0

[Xavier Periole]

in your agg2t.top you should replace the last line :
SOL    XXX
by:
Methanol XXX

which is the name of the molecule.

You should also remove the angle definition in methanol.itp. Placing
a ";" at the beginning of the line is enough.

XAvier

On Tue, 11 Dec 2007 15:40:04 +0530 (IST)
  sharada  <sharada at ccmb.res.in> wrote:
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> Dear Mark Abraham,
> I have changed MeoH to SOL in .gro and .itp files and also changed the 
>#include line  to "methanol.itp"
> It now seemed to have written the solvent molecules in the top file with SOL 
>as the name with atom types of methanol. 
> When I ran grompp program as following I get the error as shown below: I am 
>also attaching the .gro,.itp,.top files. for information.  Did I miss out 
>anything ? 
> grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr
> [asd at ccmb Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o 
>agg2_em.tpr
>                      
> Option   Type  Value  Description
> ------------------------------------------------------
>       -[no]h   bool     no  Print help info and quit
>       -[no]X   bool     no  Use dialog box GUI to edit command line options
>        -nice    int      0  Set the nicelevel
>       -[no]v   bool    yes  Be loud and noisy
>        -time   real     -1  Take frame at or first after this time.
>          -np    int      1  Generate statusfile for # nodes
> -[no]shuffle   bool     no  Shuffle molecules over nodes
>    -[no]sort   bool     no  Sort molecules according to X coordinate
> creating statusfile for 1 node...
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 141 of the 1176 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Cleaning up temporary file grompp5RBSRX
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: toppush.c, line: 1264
>Fatal error:
> No such moleculetype SOL
> -------------------------------------------------------
> I never prefer working in root as I know  the problems. Thanks for 
> suggesting. I needed to change the methanol.itp and methanol216.gro which 
>could be possible only through root. 
> regards
> sharada 
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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