VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Oct 27 2021 - 23:55:46 CDT

John's recollection is correct -- namdenergy is just a tcl script that
writes and subsequently runs a namd config file, and then parses the
output. Have you run any successful namd simulations with this system? If
so, what parameter file(s) did you use for that run? My suspicion is that
you just need to be using charmm36 parameter files (which likely match what
you used for your topologies), because that HA atom is type HB in
charmm22/27, but HB1 in charmm36.
BTW, if you want to see the script that namdenergy is using, you can set
the 'debug' flag and then edit it yourself to play with settings -- but
here I'm pretty sure it is a parameter file issue.
Best,
Peter

On Wed, Oct 27, 2021 at 11:32 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>
>