Re: Convert solvated CHARMM PDB + PSF to Amber

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Sep 17 2020 - 20:00:59 CDT

Thanks Michael,

I had good luck with charmm-gui.org. It has a force field (FF) converter:

http://www.charmm-gui.org/?doc=input/converter.ffconverter

which let me convert a CHARMM solvated system to amber parameter and
topology file. One should be aware that:

1) The input system must have been produced using the latest FF, CHARMM36
right now.

2) One must provide a CHARMM CRD file in the extended format (IOFOrmat
EXTEnded).

3) The PSF file must be in the XPLOR format (where atom types are
mentioned explicilty instead of by numbers) and the keyword XPLOR must be
present in the first line (at least older versions of CHARMM and psfgen do
not add the XPLOR keyword automatically to the first line even if the PSF
is indeed in XPLOR format, so it the PSF file needs to be edited
manually):

http://charmm-gui.org/?doc=lecture&module=pdb&lesson=6

4) You must specify the box dimensions, otherwise you get a division by
zero error.

I may check out ParmEd in the future. For now, I am happy with the output
from charmm-gui.

Best,

    Gianluca

On Thu, 17 Sep 2020, Michael Robinson wrote:

> Hello Gianluca,
>
> The ParmEd program is designed for conversion between force fields, including CHARMM and
> Amber. It may be helpful for your work:
>
> https://github.com/ParmEd/ParmEd
>
> However, it is also possible to directly use the Amber FF in NAMD, without having to
> convert anything. If you're simply trying to have your system entirely using Amber
> parameters, it might be easier to do it in this way:
>
> http://ambermd.org/namd/namd_amber.html
>
> If you're trying to mix-and-match, using some Amber parameters and some CHARMM parameters,
> that is likely to give unphysical results, and it's generally advised to avoid this method.
>
> Hopefully that's helpful,
> Regards,
> Michael Robinson
>
> On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u.washington.edu> wrote:
> Dear all,
>
> Does anybody have any recommendation how to convert a solvated system
> (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force
> field so that it can be used in NAMD with the Abmer force field
> parameters?
>
> Thanks,
>
>       Gianluca
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>                      +1 (206) 685 4435
>                      http://gianluca.today/
>
> Research Assistant Professor at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://gianluca.today/

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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