[gmx-users] ptn ptn interaction

Justin A. Lemkul jalemkul at vt.edu
Thu May 24 07:49:11 CEST 2012

On 5/24/12 7:43 AM, rethina malliga wrote:
> Hi,
> I tried protein protein simulation in gromacs.
> I prepared one ptn and kept seperately with its .top, .itp, .gro files.
> Then I prepared another protein and I build the complex of pasting the .gro file
> of first processed protein in the .gro file of second processed ptn.
> In the topol.top  of second protein I included the molecule type at the bottom
> and inserted
>    ;Include ligand topology
>    #include "posre.itp"

Be careful about name clashes here - the first protein (by default) will have a 
file named "posre.itp" that will be applied to it.  If you use the same name for 
different files, you'll probably get other errors.  I find it useful to call 
everything based on specific names, like "posre_proteinA.itp" or something similar.

> And i run succeccfully the newbox generation, solvent adding commands.
> But with the ions adding command it shows fatal error that the atoms in
> topol.top and solv.gro is different.
> `Fatal error:
> number of coordinates in coordinate file (solv.gro, 231262)
>               does not match topology (topol.top, 237548)
> on analysing the difference between two files i come to know that it is taking
> the atoms of first protein for the second protein though i named first and
> second proteins different.

After you added the second protein, did you correctly update the [molecules] 
section of the topology?

> I changed the residue information in .gro of first file to 1LIG and change
> everything regarding second molecules name as 1LIG

Unless your protein residues are all called LIG, then this is not appropriate.

> and after retrying the ions adding command it says no such molecule type found.
> `Fatal error:
> No such moleculetype 1LIG
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors

This comes from incorrect naming.  Updating [molecules] correctly with the name 
of your second protein [moleculetype] will solve it.  Make sure you make changes 
to both the coordinate file and topology at all steps - they should always match.



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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