[gmx-users] ptn ptn interaction

rethina malliga sgrm.bu at gmail.com
Thu May 24 07:43:44 CEST 2012


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"

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.

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

and after retrying the ions adding command it says no such molecule type

`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

kindly help me to trace where I m doing the mistake and to run ptn ptn


Rethina Malliga Gunasekaran,
Department Of BioInformatics,
Science Block,
Alagappa University,
Karaikudi – 630 003, India.

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