[gmx-users] Custom Force Field

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 5 23:20:02 CEST 2009

Honman Yau wrote:
> 2009/10/6 Justin A. Lemkul <jalemkul at vt.edu <mailto: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 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!


> 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


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