[gmx-users] ptn ptn interaction

[Justin A. Lemkul]

On 5/25/12 3:19 AM, rethina malliga wrote:

>     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.

> Hi Justin,
>
> I tried again with correct namings. If I leave the original name for second
> protein molecule type (Protein_chain_A) unaltered  it shows difference in atoms
> of topol.top and solv.gro. If I alter the molecule type, where ever its instance
> appears it shows molecule type not found.
>
> Thanks in advance
>

Please don't reply to the entire digest message; it becomes hopelessly 
confusing.  Your approach of leaving the original names in place is the best way 
to proceed.  As for the error that arises about coordinates and topology not 
matching, consult this document:

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

The solution is always better bookkeeping.  You may wish to start over, prior to 
solvation, and have tools like genbox and genion do all the bookkeeping for you 
by invoking the -p flag with each.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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