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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Sep 28 15:30:21 CEST 2011

On 28/09/2011 6:16 PM, Pedro Gonnet wrote:
> Hi,
> 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?

If either exists, I don't know about it.
> 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
> involved.
> 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.

A possible work-around is to copy residuetypes.dat to your working 
directory and append "POPC Lipid" to it. I expect this will inhibit the 
mechanism responsible for the unwelcome atom renaming. Please let us 
know if so.

Alternatively, I believe another work-around is to follow the general 
procedure here 
modifying the various parts of the POPC residue entry in the .rtp file 
to have atom names other than O1 and O2, and the PDB atom names to match.


> 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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