[gmx-users] Request for PDB with the same label as in Gromocs topologies.

Mikko Hellgren Mikko.Hellgren at mbb.ki.se
Tue Mar 28 18:06:40 CEST 2006

Hi David and the rest of the network! Thank you for your response and as
always I get some nice information from you. 

Ok - I understand that the problem is complicated, but the ligands that
already are in the forcefields in gromacs like NADH and Retinol, could
not the one that created the topology in whatever forcefield also
contribute with its pdb with the same atom labels as in that specific
forcefield. I mean that we could have ffG43a2.pdb for example with the
residues and ligand pdbs in it. In my work I planned to use ffG43a2 in
pdb2gmx to generate the *.gro file. But perhaps it is not as easy as I
thought to generate the pdbs for different forcefields? 

Best to David and the rest of you out there....

One cannot avoid making mistakes if one tries to produce a set of words,
or of mathematical formulae, to describe nature. Nature is more
complicated than language or mathematics. Nevertheless, one must do
one's best to produce a set of symbols which are not to discordant with
the facts.
J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949

----- Original Message -----
From: David Mobley <dmobley at gmail.com>
Date: Tuesday, March 28, 2006 5:30 pm
Subject: Re: [gmx-users] Request for PDB with the same label as in
Gromocs topologies.
To: mikko.hellgren at ki.se, Discussion list for GROMACS users
<gmx-users at gromacs.org>

> Mikko,
> If I understand correctly what you're asking (that is, what atom types
> in GROMACS correspond to what names in the PDB) this is really
> nontrivial and there isn't one answer. In particular, each force field
> has its own set of atom types. There are, for example, many different
> types of carbon atoms that have different parameters depending on what
> they are bonded to. Different force fields use different numbers of
> atom types (which also have different names). Figuring out what atom
> types you should use for a particular ligand isn't simply a matter of
> figuring out which atom types correspond to which PDB names, as there
> may not be a 1:1 correspondence (in particular, one PDB name may
> become three different atom types in one force field, four in another,
> and six in another). Then you have to somehow figure out what atom
> type is the best for the molecule you are considering. This is one of
> the particularly nasty parts of running calculations with ligands:
> Coming up with parameters for the ligands is nontrivial.
> Depending on what force field you are using, there may be automated
> ways of doing this. I know a number of docking people who are using
> the OPLS force field, and they must have some automated way of doing
> "atom typing" for their ligands. (Atom typing is, if I understand your
> question right, what you're talking about: Coming up with what atom
> types best represent the atoms in the molecule of interest given a PDB
> file). I don't know what utility people do for that. Another approach
> is to use the AMBER force field (which the Pande group has ported to
> GROMACS) and then develop ligand parameters using the ANTECHAMBER
> package (which you can download online) with the GAFF (Generalized
> Amber Force Field) for small molecules. These come out in AMBER
> format, though (different units, etc) and need to  be converted to
> GROMACS. A third approach is to use an online server that can generate
> topologies for your ligand of interest. For example, prodrg can take
> pdb/mol2/other files for ligands and generate certain
> GROMACS-compatible topologies (but only for certain force fields).
> I hope that gets at what you're trying to do. Basically the upshot is
> that you need to decide what force field you want to use, and then
> figure out how to do the atom typing appropriate for that force field.
> An additional caveat is that you should make sure your ligand
> parameters are compatible with the protein force field you are using
> (that is, it would probably be a bad idea to use OPLS parameters 
> for a
> ligand while using AMBER parameters for a protein, or some such).
> If you decide you want to use the AMBER force field, I can probably
> give you a bit of help on generating GAFF parameters for your small
> molecules; contact me off list. I don't have any experience with other
> force fields at this point so you would be better off looking
> elsewhere if  you want to use OPLS.
> Incidentally, aside from getting force field parameters somewhere, you
> may or may not need to also compute partial charges (I think in OPLS
> partial charges are more or less linked to the force field, but this
> isn't very much the case if you use GAFF or prodrg).
> David
> On 3/28/06, Mikko Hellgren <Mikko.Hellgren at mbb.ki.se> wrote:
> > Hi all Gromacs users and developers, I wonder if anybody has pdb 
> files> for NAD+ (NADH in Gromacs), NADH (NADP) and Retinol (RTOL) 
> with the same
> > labels as in Gromacs topologies. This would save me a lot of time 
> in my
> > work since the atom names in my PDB for the ligands are different 
> from> Gromacs atom names, and it would take me a lot of time to 
> figure out how
> > to make them consistent to each other.
> >
> > I think it would be great if the developers of all the topologies in
> > Gromacs also could submit the pdb file of the topology. This 
> would save
> > time (at least to me :-)) and help me to understand what all atom 
> names> in gromacs topologies stand for. I know that the problem of 
> different> atom labels is not due to Gromacs but it is the reason 
> for the need of
> > pdb:s for all molecules with topologies in Gromacs.
> >
> > If there is some other way to relabel atom names in an easy 
> fashion, I
> > would be very great full for any advice on that also.
> >
> > Best,
> > Mikko Hellgren
> > PhD student at Karolinska Institutet
> > mikko.hellgren at ki.se <------- if you have the pdb I want, please 
> send it
> > to me.......
> >
> >
> >
> >
> >
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> >
> >
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