[gmx-users] Covalent bonds between topology files

[Tsjerk Wassenaar]

Hi W. Allen,

This is not necessarily a problem. The gb_* labels can be found in the
ffG*bon.itp files, and are replaced by the values found in those files
upon preprocessing. If they both correspond to the same force field,
it's no problem to combine them with some parameters referred to by
codes and others written in full. You may have to worry though,
regarding the force field used for both files. This should be the same
for both.

Best,

Tsjerk

On 9/26/06, wjallen at vt.edu <wjallen at vt.edu> wrote:
>
>
> Thank you for your reply, Mark.  That is what I was afraid of, that I would have
> to physically combine the files.  My only problem there is the format of the
> topology file that comes from pdb2gmx is slightly different than that which
> comes from the PRODRG server.  For example, under the  [ bonds ]  section:
>
> (from pdb2gmx):
> ...
> 5234  5236    2    gb_2
> 5237  5238    2    gb_4
> ...
>
> (and from PRODRG):
> ...
> 5252  5254    1     0.140   334720.0   0.140   334720.0   CAY   NBN
> 5254  5255    1     0.100   374468.0   0.100   374468.0   NBN   HAF
> ...
>
> I will try to decipher this and see what comes of it.  Thankfully, the
> renumbering of atoms was not a problem because of the reorder.pl script
> available in the user contributions section.  Again, thank you for your reply
> Mark, I hope all that I said has made sense.
>
> Cheers,
> W. Allen
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-- 
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336