Honman Yau wrote:
2009/10/6 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@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 correctly?
These files may not all be necessary (particular .ddb, -n.tdb, and -c.tdb), but
.rtp, .hdb, nb.itp, bon.itp, etc. are not protein-specific. They define
residues and parameters within a given force field.
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?).
If you haven't created the corresponding force field files, you can certainly
expect that magic won't work :)
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.
I suppose it's a matter of choice. It's just about the same amount of work
either way, really. Any future users would simply have to #include the .itp
files you come up with, and never have to worry even about using pdb2gmx!
-Justin
Once again, thank you very much and, again, thank you very much in advance!
Kind regards
Honman
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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