Re: Issue using qwikMD with an uncommon cofactor

From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Thu May 31 2018 - 17:55:02 CDT

Hi Benjamin,
Unfortunately, QwikMD was created to use the latest FF (in this case, 36).
There are many reasons why, including many researchers and journals who
won't even accept manuscripts that use CHARM22.

The reason why you can't easily get the files created by QwikMD and just
change the NAMD configuration file to use CHARM22 is because the PSF files
were created assuming the CHARM36 topologies and parameters, which use a
different naming for some atoms.

My suggestion, for a "first pass", would be to create a new parameter file
approximating the CHARM36 naming, but using your CHARM22 parameters. This
WILL NOT be a scientifically sound system due to the inconsistencies in
parameters (your active site parameters would ultimately need to be created
in the CHARM36 context) but will at least allow you to create and probe
your system with NAMD and VMD, to make sure there aren't any other issues.
Maybe others can provide other suggestions.

FYI, it would be important to have good parameters because you should
equillibrate your system before initiating any QM/MM, but it may be that
your QM region will cover the residues that need parameters, in which case
those parameters will be completely ignored.

Hope this helps,
Marcelo

P.S. I'm also replying to the NAMD mailing list so others can find this in
the future.

---
Marcelo Cardoso dos Reis Melo
PhD Candidate
Luthey-Schulten Group
University of Illinois at Urbana-Champaign
crdsdsr2_at_illinois.edu
+1 (217) 244-5983
On 31 May 2018 at 17:27, Benjamin Rousseau <benjamin.rousseau_at_duke.edu>
wrote:
> Hello,
>
>
> I am trying to use NAMD's QM/MM feature, and I thought I would do well to
> use qwikmd to make the simulation scripts.
>
>
> My protein (PDBID: 1sdw) has an uncommon active site, the only parameters
> (that I know of) for which are intended to run with CHARMM22 force fields.
> In addition, the psf I generated for previous classical MD required the use
> of many "PATCH" statements. I am getting error messages in qwikmd that I
> suspect are due to its assumption that I'd like to use CHARMM36 force
> fields. I have tried to overwrite these FF, even changing the source code
> to load CHARMM22 force fields. However, this hasn't proven successful.
>
>
> Have you heard of this type of issue with qwikmd? Do you know how I might
> go about overriding this preference for CHARMM36 force fields?
>
>
> Thank you for your time and help,
>
> Ben
>

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