[gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?

[J. Nathan Scott]

Hello all! I spent some time searching the archive and can't find an
answer to this question. Is there a replacement for the -rtpo option
for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am
using) manual (pg 115) but does not seem to work, and yields the error
"Invalid command line argument: -rtpo" when I try to use it

I would basically like to have the OPLSAA aminoacids.rtp file in my
working directory (which has some modified charges for the TRP
residue) supersede the one in the Gromacs force field share directory.
Is there a way to do this?

So far I have resorted to copying the shared oplsaa.ff folder to my
working directory and modifying the aminoacids.rtp file in that
directory, and then selecting that directory to source my force field
when I run pdb2gmx. This of course works, but I have noted a peculiar
behavior using this method. No matter whether I select force field 1,
which is OPLSAA from my working directory, or force field 15, which is
OPLSAA from the share directory, my topology file ends up with charges
in the working directory oplsaa.ff folder's aminoacids.rtp file. Even
when I select that pdb2gmx should use the share version, it is clearly
still using the force field folder in my working directory. I
confirmed this by renaming the aminoacids.rtp in the working directory
file to aminoacids.rtp.bak, which produced the error "Could not find
any files ending on '.rtp' in the force field directory 'oplsaa.ff'"

Can someone recommend a better method for what I am attempting to do?
Also, is pdb2gmx's handling of force field directories appropriate? I
had assumed that selecting the share version of a force field would
force all the necessary files to be read from that share directory,
but this is clearly not the case.

-- 
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J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University