VMD-L Mailing List

From: Alexei Rossokhin (alrossokhin_at_REMOVE_yahoo.com)
Date: Thu Oct 28 2021 - 09:14:27 CDT

 Dear Peter,thank you for your help. Now it works properly.Alexey

    On Thursday, October 28, 2021, 03:56:49 PM GMT+3, Peter Freddolino <petefred_at_umich.edu> wrote:
 
 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)Best,
Peter

On Thu, Oct 28, 2021 at 3:27 AM Alexei Rossokhin <alrossokhin_at_yahoo.com> wrote:

 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 <petefred_at_umich.edu> 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 <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
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