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, [EMAIL PROTECTED] <[EMAIL PROTECTED]> 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
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