From: Peter Freddolino (
Date: Thu Oct 28 2021 - 07:56:37 CDT

Hi Alexey,
Please keep the email list copied on your replies. You'll want to get a
file like par_all36_prot.prm, which is available from the charmm force
field webpage or included with vmd (plugins/noarch/tcl/readcharmmpar1.3)

On Thu, Oct 28, 2021 at 3:27 AM Alexei Rossokhin <>

> Hi Peter,
> thank you very much for your response. I also think the problem is in
> choosing the prameter file. QwikMD generated my project with charmm36 and
> MD started and run successfully. NamdEnergy loads
> par_all27_prot_lipid.inp by default and I have a problem with atom types. Tell
> me which parameter file is analogous to charm36. I tried different ones
> like top_all36_prot.rtf but got an error like "unkown line 36 1".
> Alexey
> On Thursday, October 28, 2021, 07:57:44 AM GMT+3, Peter Freddolino <
>> wrote:
> (probably implicit in what I just said, the most important thing is that
> your parameters match the topology that you used -- and in this case, I'm
> pretty sure that means use charmm36)
> On Thu, Oct 28, 2021 at 12:55 AM Peter Freddolino <>
> wrote:
> 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 <> 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:
> > 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
> Phone: 217-244-3349