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

[Tsjerk Wassenaar]

Hi,

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
by pdb2gmx.

Hope it helps,

Tsjerk

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).
>> 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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>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist