From: Michael Robinson (michael.robinson1_at_monash.edu)
Date: Fri Sep 18 2020 - 02:22:16 CDT
Hi Gianluca,
Thanks for getting back to the mailing list with a solution to your issue!
Helpful for anyone who comes across this in the future.
Regards,
Michael
On Fri, 18 Sep 2020 at 11:01, Gianluca Interlandi <gianluca_at_u.washington.edu>
wrote:
> 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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