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. <br>
<br>
<div class="gmail_quote">On Fri, Jan 29, 2010 at 6:24 AM, Alan <span dir="ltr"><<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Dear Berk,
<div><br></div>
<div>I beg your pardon, but I have to assume that what you wrote below is not correct so, right?</div>
<div><br></div>
<div>Should it be 'ligand.rtp' instead of 'ligand.itp'?</div>
<div><br></div>
<div>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).</div>
<div><br></div>
<div>Cheers,</div>
<div>Alan
<div class="im"><br><br>
<div class="gmail_quote">On Fri, Jan 29, 2010 at 11:00, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div>> of them. So you can just put, e.g., a file called ligand.itp in your force<br>> field or current dir and pdb2gmx<br>> will read it.<br></div></blockquote></div><br><br clear="all"><br></div>
<div class="im">-- <br>Alan Wilter Sousa da Silva, D.Sc.<br>PDBe group, PiMS project <a href="http://www.pims-lims.org/" target="_blank">http://www.pims-lims.org/</a><br>EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK<br>
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