Hi,
I too encountered simillar problem earlier. I found solution by
myself by the following way. I hope you are running gromacs in
windows under cygwin or running Gromacs in any of the unix based
system and editing your file topology file in windows editor (eg.
notepad or wordpad). If it is the case simply run
>dos2unix drg.top under the command mode and try to use that top file(your case
>drg.top). Hope it will fix your problem.
Good luck !
B.Nataraj
On Thu, 02 Mar 2006 13:01:35 +0100, "Dariusz Plewczynski"
<[EMAIL PROTECTED]> said:
>
>
> Dear Sirs,
>
> I have a problem with running the short simulation with GROMACS. I have
> a structure for a small ligand (drg.pdb after cleaning with PRODRG). For
> this ligand I have run PRODRG in order to get drg.gro file and drg.itp
> topology file. I have edited the drg.top in order to include drg.itp as
> #include. My goal is to run simulation in vacuum (no water) - with only
> ligand (!). No protein also. I have tried to run it but I am getting
> error message. It seem that GROMACS does not read my topology file. What
> I am doing wrong ?
>
> grompp -f em.mdp -c drg.gro -p drg.top -o drg.tpr
>
>
> Results:
> ....
>
> creating statusfile for 1 node...
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (drg.gro, 25)
> does not match topology (drg.top, 0)
>
>
> Regards
>
> Dariusz
--
raja
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