[gmx-users] Custom Force Field
jazzycafe at gmail.com
Mon Oct 5 20:38:10 CEST 2009
2009/10/6 Justin A. Lemkul <jalemkul at vt.edu>
Hi again! Thank you very much for the swift reply!
> If you want to use pdb2gmx, you will need to create all the standard files
> (.rtp, .hdb, nb.itp, bon.itp, etc), create an entry in FF.dat, and increment
> the counter at the top of FF.dat.
Ah, I'm actually already in the process of writing a script to do that
convert my force field files. :) Regarding this though (which I just
realised that I should also have asked earlier) - since I am not actually
doing any protein simulations or anything that has amino acids in it, do I
still need the the *.rtp*, *.hdb*, *.ddb* files for *pdb2mgx* to work
I did try to increment the counter at the top of *FF.dat* before I sent the
last e-mail but it didn't seem to work (or is that because I was missing
> Otherwise, it is relatively simple to write your own topology for a limited
> number of species as .itp files. See Chapter 5 of the manual for the format
> and requirements of all of these files.
I have considered that option and read the manual already. :) It seems to
be easier (for someone else who will be picking up where I will have left
off) that I get the script running and have *pdb2gmx* do the job.
Once again, thank you very much and, again, thank you very much in advance!
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