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Hi,<br><br>I think that what you are referring to is something different.<br>What I have added is that you can easily add rtp files, not itp files.<br>For many force fields it is actually much simpler and less work to write rtp files than itp files.<br>So the things I have implemented might help. But they would not if you can only<br>generate itp files.<br><br>If you only have an itp file, you would need to strip the molecule out of the pdb beforehand,<br>or pdb2gmx should know how to like a certain residue type (?) to an existing itp file.<br><br>Berk<br><br><hr id="stopSpelling">From: alanwilter@gmail.com<br>Date: Fri, 29 Jan 2010 09:40:20 +0000<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Re: including a custom itp file in topology<br><br>Hi Berk,<div><br></div><div>If pdb2gmx will do what you said below, then for me the feature is delivered.</div><div><br></div><div>To be sure, what I would like to have (and I guess Jack too) is:</div><div><br></div><div>- one has a pdb with protetin + ligands (one or more)</div>
<div>- have the topologies itp files for the ligands already created</div><div>- run pdb2gmx on complex.pdb and have pdb2gmx to *know* about the ligands and generated the respective top and gro files ready for EM and MD.</div>
<div><br></div><div>It is that what I understood Jack wants and what you said you have added to the coming pdb2gmx (for gmx 4.1?).</div><div><br></div><div>Many thanks,</div><div><br></div><div>Alan<br><br><div class="ecxgmail_quote">
On Fri, Jan 29, 2010 at 09:28, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div id="ecx:164" class="ecxii ecxgt">
From: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
<br>
Hi,<br>
<br>
I don't understand exactly what is the requested feature here.<br>
I am currently reorganizing the force field setup in Gromacs to more cleanly support AMBER and CHARMM<br>
and adding some extra functionality. I started a discussion on the gmx-developers list on this topic.<br>
On feature I have added is that rtp, hdb, etc files no longer have fixed names and you can have multiple<br>
of them. So you can just put, e.g., a file called ligand.itp in your force field or current dir and pdb2gmx<br>
will read it.<br>
<br>
Berk<br></div></blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter Sousa da Silva, D.Sc.<br>PDBe group, PiMS project <a href="http://www.pims-lims.org/">http://www.pims-lims.org/</a><br>EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK<br>
+44 (0)1223 492 583 (office)<br>
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