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On 15/04/2012 9:54 PM, Marc Gordon wrote:
<blockquote
cite="mid:CA+dsNkxM1Zy7PqZiM=zgz7ncYRUuqmSMGKwsf+3a5OVifOc4Jg@mail.gmail.com"
type="cite">Here is a brief summary of my situation:<br>
<br>
From what my copy of gromacs tells me pdb2gmx is using a 53a6
forcefield from 2004.<br>
I want to use the more recent carbohydrate specific 53a6_carbo
force field.<br>
I have only managed to find this force field in GROMOS format.<br>
<br>
What I ultimately want is just the gromacs input topology files
etc. generated by pdb2gmx (or some other equivalent application).
I don't intend to actually run the simulation in gromacs, for that
I will be using NAMD but I need the gromacs input files in order
to perform the run through 53a6_carbo.<br>
<br>
So as far as I can see I have a few options and I wanted to seek
the advice of those with more experience than myself in the use of
gromacs and associated applications:<br>
1. someone has done this already and is willing to share<br>
2. convert GROMOS force field format (.mtb and .ifp) into gromacs
format (.rtp, .itp, .atp etc.) and then incorporate that into
pdb2gmx - if some sort of application exists for this then great
otherwise it seems like a rather complicated task (not the
incorporating but the converting)<br>
</blockquote>
<br>
Useful conversion programs tend to be rare, but they do exist. No
idea if one useful for you exists. Google hard, and contact the
authors of the force field to see what they know about who might
have anything useful.<br>
<br>
<blockquote
cite="mid:CA+dsNkxM1Zy7PqZiM=zgz7ncYRUuqmSMGKwsf+3a5OVifOc4Jg@mail.gmail.com"
type="cite">
3. amend the existing 53a6 force field in pdb2gmx to incorporate
the desired carbohydrate elements - is such a thing possible?<br>
</blockquote>
<br>
Yes, the last para of the approach here <a
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a>
is appropriate to this. If there's only a small subset of the
changes to 53a6 that are relevant for your simulation, this is
probably the simplest approach.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CA+dsNkxM1Zy7PqZiM=zgz7ncYRUuqmSMGKwsf+3a5OVifOc4Jg@mail.gmail.com"
type="cite">4. use something other than pdb2gmx that performs the
same function<br>
<br>
Any suggestions would be appreciated.<br>
<br>
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<br>
</blockquote>
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