VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 27 2021 - 21:32:37 CDT

Hi,
  My recollection is that the NAMDEnergy plugin works as a wrapper
around NAMD, and it is expecting that the molecule as defined in
VMD was a system that was already prepared for an MD simulation,
and therefore all of the atom types etc are properly set. You would
need to use only such files as input, and you wouldn't be able to
just load a PDB and run it. If you've used QwikMD to prepare a
set of NAMD input files, then you'll want to ensure that you start
by loading only those files into a molecule before you try and
run NAMDEnergy on it. That's about the only advice I have for you.

Best,
  John Stone

On Tue, Oct 26, 2021 at 11:19:49AM +0000, Alexei Rossokhin wrote:
> Dear VMD community,
> I am new to NAMD and VMD.
> I use VMD for WIN32, version 1.9.3 (November 30, 2016) and generated my
> psf and conf files using VMD QwikMD.
> Can anyone advise me on how to do partitioning of energy? When I use the
> plugin NAMDEnergy and par_all27_prot_lipid.inp as a parameter file I am
> having problems with atom types, with the following error:
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HB1
> Below is a line from my psf file
> 6 AP1 19 LYS HA HB1 0.100000 1.0080 0
> Is this the correct HB1 type? Maybe the type should be HA?
> Thank you in advance,
> Alexey 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/