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

[sharada]

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 

                                
                            
                        
                        
                    
                
            
            
        
    

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071211/9b75e7c2/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: methanol.itp
Type: application/octet-stream
Size: 1217 bytes
Desc: methanol.itp
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071211/9b75e7c2/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: methal216.gro
Type: application/octet-stream
Size: 2516 bytes
Desc: methal216.gro
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071211/9b75e7c2/attachment-0001.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: agg2_b4emt.gro
Type: application/octet-stream
Size: 4327 bytes
Desc: agg2_b4emt.gro
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071211/9b75e7c2/attachment-0002.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: agg2t.top
Type: application/octet-stream
Size: 8381 bytes
Desc: agg2t.top
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071211/9b75e7c2/attachment-0003.obj>