[gmx-users] GBSA with ligands
leandro.obt at gmail.com
Fri Oct 12 15:03:13 CEST 2012
thank you for the reply.
I have already read the previous related questions, but thanks for
pointing that out anyways. I will develop my doubt further here.
According to what I saw in the list I can simply borrow the parameters
from the force field gbsa.itp in a chemical homology-like way. Is there an
automated way to do it? A script maybe...
Additionally, how about other atom types? e.g. there isn't parameters
for the fluorine, bromine or phosphorus atoms in any gbsa.itp, which are
used in some ligands.
And, more fundamentally, can you suggest some literature about how to
derive GBSA parameters ab initio?
2012/10/12 Alan <alanwilter at gmail.com>
> Hi, the issue is not with Antechamber or Acpype. There were similar
> questions to yours here (try searching GMX mail archives). The problem is
> you need to create the GBSA.itp parameters for you ligand.
> Which Acpype does is to create/convert Amber/GAFF parameters to usual MD in
> On 12 October 2012 11:34, Leandro Bortot <leandro.obt at gmail.com> wrote:
> > Dear users,
> > After parametrizing a ligand with antechamber and converting the
> > topology and structure files with acpype I can't do GBSA simulations in
> > GROMACS because of missing GB parameters. In fact, the implicit solvent
> > parameters weren't converted from the AMBER topology (.prmtop) to the
> > GROMACS topology (.top) by acpype.
> > There is a "FLAG RADII" in the .prmtop but there is no [
> > implicit_genborn_params ] in the .top.
> > Is this an issue with acpype?
> > Any help would be greatly appreciated
> > Best regards,
> > Leandro
> > --
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> Alan Wilter SOUSA da SILVA, DSc
> Bioinformatician, UniProt - PANDA, EMBL-EBI
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