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

[Mark Abraham]

On 8/12/2010 4:07 AM, J. Nathan Scott wrote:
> 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 is the intended behaviour. Rather than modifying your installed 
database, or having to mess with the GMXLIB environment variable, you 
can copy the whole xx.ff directory into a local directory and have local 
modifications. pdb2gmx reports clearly on stdout which directory(s) it 
is (considering) using.

>   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'"

That sounds very weird. I'd suggest you start a new working directory, 
copy the oplsaa.ff over fresh, make the .rtp modifications and see if 
you can reproduce the issue. If so, please file a Bugzilla.

> 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.

It should be the case.

Mark