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
--
========================================
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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