[gmx-users] Re: Fwd: itp file problem

Justin A. Lemkul jalemkul at vt.edu
Fri May 18 15:39:27 CEST 2012

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor and will soon be leaving for a trip and will have limited access 
to email, so relying on me for personal help is a bad choice at this time.

On 5/18/12 9:30 AM, Sarath Kumar Baskaran wrote:
> Dear Justin Sir,
> I am very sorry to trouble u this much, but as u said i tried to run the
> simulation of the Protein ligand complex with the new gromos96 43a1 in version
> of GROMACS 4.5
> its again showing the error that atom type mistmatch between prtb4ion.pdb and
> prt.top

I don't know what this means.  Please copy and paste all relevant error messages 
rather than try to interpret them yourself.

> i checked each and every line of the top, the error is due to the itp file where
> there are 5 atoms extra which is not in normal DRGPOH.pdb resulting in prtb4ion.pdb
> This is really very troublesome. Please Please help me.....

The coordinates and topology from PRODRG should match.  If they don't, you 
downloaded the wrong file(s).  Gromos96 43a1 has explicit representation of 
polar and aromatic hydrogens.  I suspect there's some mismatch there, but only 
you know what the extraneous atoms are.

> Also i am getting the same error in with the gromos96 43a1 in version of GROMACS
> 4.0.5, which i used for previous simulations with other ligands....
> trying editing the .itp file with that extra atoms results in a Warning that
> bonds section of itp file in not for this molecule...... What to do sir.....

Clear up the problem with the .itp file above and this will be solved.  Hacking 
the topology is not the correct solution.  Obtaining the correct files is.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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