Would it be possible to add some capping residues (like --COCH3 and --NHCH3) by writing a separate .itp file and including it in the topology file? Is there a way to make it consistent with charmm forcefield?<div><br></div>
<div>Can this be done alternatively by modifying the .rtp file? If yes, what other operations must one do before using these .rtp files?</div><div><br><div class="gmail_quote">On Wed, Jun 30, 2010 at 8:39 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br><br>----- Original Message -----<br>From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
Date: Thursday, July 1, 2010 9:58<br>Subject: Re: [gmx-users] Capping residues<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br>> <br>
> <br>> Sai Pooja wrote:<br>> >Hi,<br>> ><br>> >1) What capping residues are recognized by charmm implemented <br>> on gromacs in the latest git version?<br>> <br>> It looks like there aren't any. Check the .rtp file to be sure.<br>
<br></div>There aren't. I had a discussion with Par Bjelkmar a while back about including some, but I don't recall the outcome.<br><font color="#888888"><br>Mark</font><div><div></div><div class="h5"><br><br>> >I was trying to use ACE for acetyl but it is not recognized by <br>
> pdb2gmx.><br>> ><br>> >2) Is it possible to define caps at residues other than those <br>> at the termini?<br>> ><br>> <br>> What exactly do you consider a cap? Usually a capping <br>> residue is applied only to N- and C-termini. If you're <br>
> trying to make some sort of modified sidechain, then you have to <br>> look into parameterizing it yourself.<br>> <br>> <a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
> <br>> -Justin<br>> <br>> >Regards<br>> >Pooja<br>> ><br>> >-- <br>> >Quaerendo Invenietis-Seek and you shall discover.<br>> ><br>> <br>> -- <br>> ========================================<br>
> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> -- <br>
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