2009/10/6 Justin A. Lemkul <[email protected]> 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 correctly? 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 files?). > 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 Honman
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