From: Peter Freddolino (
Date: Tue Feb 05 2008 - 06:51:37 CST

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?


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
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