[gmx-users] dimerization problem

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 31 14:21:24 CEST 2008

prasun kumar wrote:
> Dear user,
> I want to check the dimerization of a peptide chain having 227 
> residues.I am doing the following steps:
> 1. First i transformed the given peptide by 20 angstrom by     
>    modifying corresponding pdb file and save it as
>    f1.pdb(say),original file given was 'f.pdb'(say)
> 2 .Now i run the pdb2gmx command for both the proteins.
> 3 add the two files and remove the END of one of the file(i   
>    mean   to say i remove the END from the middle).
> 4. Now run the EDITCONF command
> 5 Modify the topology file in the molecules section by
>    replacing 1 by2.
> 6 run the grompp command and mdrun for energy
>    minimization for 2000 steps.
> 7 again run grompp for positional restrained dynamics
> till here every thing work
> but when i tried to run mdrun its telling your protein is not minimizd 
> properly.
> after  this I tried another method by modifying opology file in the 
> following way

If your system isn't minimized properly, changing the format of the topology 
won't fix it.  You've probably got some type of steric clash that can't be 
resolved.  Did energy minimization cut off at 2000 steps, or did it complete 
before that?  You could always try running more EM if it ended at 2000.

> I added one proteins topology file in the another one by adding line 
> INCLUDE f1_top1.top(topology file name)
> again its working till grompp(pr)
> now when i am trying to run mdrun its givin following error
> Found a second defaults directive, file 
> "/usr/share/gromacs/top/ffG43a1.itp", line 6
> What to do?

Consult the wiki, the answer is there:



> I am not getting any other way.Please help me.
> Thanx in advance
> Regards
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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