[gmx-users] GROMACS Error

[Mark Abraham]

Not sure - perhaps if you've edited this file by hand (or in an
inappropriate editor) there's a tab-vs-space issue, or missing line ending
on the final line.

Mark

On Fri, Feb 8, 2013 at 7:40 PM, Asma Mushtaq <ashima.ashia at gmail.com> wrote:

> Dear All,
>
>
>
> I need to add 6 CL ions to make the system neutral but when I type the
> command line
>
>
>
> genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6
>
>
>
> and choose group 15 (SOL), the error is
>
>
>
> Fatal error:
>
> No line with moleculetype 'SOL' found the [ molecules ] section of file
> ‘topol.top’
>
>
>
> but when I check the ‘topol.top’ file I found there are 24504 SOL molecules
> present.
>
>
>
> My topology file looks like this
>
>
>
> ; Include water topology
>
> #include "amber99sb.ff/tip3p.itp"
>
>
>
> #ifdef POSRES_WATER
>
> ; Position restraint for each water oxygen
>
> [ position_restraints ]
>
> ;  i funct       fcx        fcy        fcz
>
>    1    1       1000       1000       1000
>
> #endif
>
>
>
> ; Include topology for ions
>
> #include "amber99sb.ff/ions.itp"
>
>
>
> [ system ]
>
> ; Name
>
> Protein
>
>
>
> [ molecules ]
>
> ; Compound        #mols
>
> Protein_chain_A      1
>
> ATQwild              1
>
> SOL                  24504
>
>
>
>
>
> Please let me know how to rectify the problem
>
>
>
>
>
> regards,
>
>
>
> Ashima
> --
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