[gmx-users] ligand in vacuum trajectories (PRODRG)

raja raja_28 at fastmail.us
Thu Mar 2 14:18:25 CET 2006

    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 !
On Thu, 02 Mar 2006 13:01:35 +0100, "Dariusz Plewczynski"
<darman at bioinfo.pl> 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_28 at fastmail.us

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