[gmx-users] Re: including a custom itp file in topology
tsjerkw at gmail.com
Fri Jan 29 14:07:25 CET 2010
rtp stands for 'Residue ToPology' and is used exclusively for building
block definitions, which are only used by pdb2gmx.
itp stands for 'Include ToPology' and can contain any part of a
topological description of a system, atom types, bond types,
moleculetypes, definitions, to be #included at the right point in the
master topology file. It is often used to separate out moleculetype
definitions, but also the top level force field parameters are
contained in a .itp file (ffoplsaa.itp for example).
For non standard residues, the residue has to be defined as a building
block and put in to a .rtp file in order to allow pdb2gmx to process
it. Non-bonded ligands need not be processed by pdb2gmx. With a proper
description in terms of coordinates and [ moleculetype ] (.itp file),
they can be easily merged with coordinates, c.q. topology as produced
Hope it helps,
On Fri, Jan 29, 2010 at 1:45 PM, Jack Shultz <js at drugdiscoveryathome.com> wrote:
> 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).
>> 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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Tsjerk A. Wassenaar, Ph.D.
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