[gmx-users] Re: including a custom itp file in topology

Jack Shultz js at drugdiscoveryathome.com
Fri Jan 29 13:45:49 CET 2010

I confess I don't know the difference between rtp and itp. What I was hoping
was an easier way to generate topologies for complexes that have
non-standard residue names like LIG. Alan's acpypi works. You just have to
do some extra scripting. But it seems like pdb2gmx should have a way to load
the files describing the non-standard residue names directly.

On Fri, Jan 29, 2010 at 6:24 AM, Alan <alanwilter at gmail.com> wrote:

> Dear Berk,
> I beg your pardon, but I have to assume that what you wrote below is not
> correct so, right?
> Should it be 'ligand.rtp' instead of 'ligand.itp'?
> Once I have my hands on this new pdb2gmx, I believe I can tweak acpypi to
> generate rtp files as well (but hdb and else probably not).
> Cheers,
> Alan
> On Fri, Jan 29, 2010 at 11:00, <gmx-users-request at gromacs.org> wrote:
>> > of them. So you can just put, e.g., a file called ligand.itp in your
>> force
>> > field or current dir and pdb2gmx
>> > will read it.
> --
> Alan Wilter Sousa da Silva, D.Sc.
> PDBe group, PiMS project http://www.pims-lims.org/
> EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
> +44 (0)1223 492 583 (office)
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