From: Irene Newhouse (
Date: Tue Feb 05 2008 - 12:46:40 CST

It turned out to be silly. I was trying to flag amber explicitly & it didn't like it. I'm up & running now, thanks!
Irene> Date: Tue, 5 Feb 2008 06:51:37 -0600> From:> To:> CC:> Subject: Re: vmd-l: VMD, NAMDenergy & AMBER parameters> > Hi Irene,> > I'm not quite sure why you're having problems. When you use namdenergy > with selections, you can have an input trajectory that contains more > atoms than you actually want to consider; a large part of the utility > comes from the fact that it will flag the atoms you actually want (via > the sel1 and sel2 arguments) so that pairinteractions in NAMD only > considers those atoms. As long as you're using a recent (I believe 1.8.6 > or later) version of vmd, you should just be able to feed it a structure > with prmtop file and it will work. So, you're run should look something like> > namdenergy -vdw -sel $proteinsel $withinsel> (with a -updatesel flag added if you want the selections to be updated > throughout the trajectory -- you'll need to grab one of the 1.8.7 > alphas off of biocore to get access to this flag)> > Does this make more sense?> > Best,> Peter> > Irene Newhouse wrote:> > I'm trying to do NAMDenergy with a trajectory obtained from NAMD, but > > using AMBER parameters. Where I run into trouble is that I have a very > > large system, but the interaction energy [ligand with protein] I want > > to calculate only encompasses a small part of it.> > > > Here's my dilemma: I select the trajectory fragment of interest using > > the "within" command. I set the value to 20A because the default > > cut-offs for NAMDenergy are less than that. I write an idx file to > > use with catdcd & a pdb file that contains the atoms selected.> > > > NAMDenergy wants either a psf file, which I can't do because my ligand > > contains atoms for which there are no CHARMM parameters, which is why > > I used AMBER parameters in the first place, or a prmtop file. When I > > take the pdb file into tleap to create a prmtop with the same number > > of atoms as my subsystem, it fills out the partial residues. So now > > the number of atoms doesn't match the dcd file any more.> > > > I'd be grateful for any advice around this problem, including a > > pointer to specific instructions how to run NAMDenergy in command line > > mode with AMBER parameters. [Then I could use the whole trajectory].> > > > Thanks so much!> > Irene Newhouse> >> > ------------------------------------------------------------------------> > Helping your favorite cause is as easy as instant messaging. You IM, > > we give. Learn more. > > <>
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