VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Oct 27 2021 - 23:57:32 CDT

(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 <petefred_at_umich.edu>
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 <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/
>>
>>