[gmx-users] ApoA1 benchmark or reading CHARMM topologies in gromacs

Pedro Gonnet gonnet at maths.ox.ac.uk
Wed Sep 28 10:16:07 CEST 2011


Short summary: Is there a gromacs version of the NAMD ApoA1 benchmark
somewhere and if not, what tools can I use to convert CHARMM
parameter/topology files to gromacs?

Now for the long version: I'm currently trying to "port" the popular
ApoA1 benchmark used by NAMD and Desmond to gromacs. I have the input
files for NAMD (they can be downloaded from
http://www.ks.uiuc.edu/Research/namd/utilities/apoa1/), i.e. a PDB and
PSF file as well as the corresponding .xplor force-field parameter
files. I also have the underlying CHARMM topology files for the lipids

I've tried generating gromacs input files using pdb2gmx, using the
CHARMM27 force-field therein. This doesn't work due to an "Atom OXT in
residue GLN 243 was not found" error which seems to be an occurrence of
bug #567 (http://redmine.gromacs.org/issues/567), yet it can't be
circumvented by replacing the type of of the OT2 atom.

I tried using the OPLS force field instead (after replacing HSD with HIS
and other minor modifications in the .pdb), but this fails with the same
error as above. If I don't include chain ids in the pdb, then it fails
since it does not recognize the POPC lipid residues. I have the CHARMM
topology files for these, but I have no idea how to convert these to
gromacs topologies.

Now, since the ApoA1 benchmark is quite popular, I'm assuming somebody
might already have a gromacs version out there... Is this the case?

If not, Is there some tool to convert CHARMM input, i.e. parameters and
topologies, to gromacs? I've found and successfully used Mark Abraham's
Perl script to convert the parameters. Therein he refers to a script by
Yuguang Mu to convert topologies, which apparently used to be on the
gromacs site
(http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz), but
which seems to have disappeared.

Many thanks and kind regards,
Pedro Gonnet

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