[gmx-users] Custom Force Field

Honman Yau 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!

Kind regards

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091006/dcdbc3ea/attachment.html>

More information about the gromacs.org_gmx-users mailing list