From: Irene Newhouse (
Date: Mon Feb 04 2008 - 17:23:37 CST

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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