Hi, Jason,
I am able to use ParmEd to create prmtop file this time from the most
recent CHARMM c36 force filed. But when I run pmemd.cuda, there was SHAKE
problem:
Number of triangulated 3-point waters found: 0
There are supposed to have 7867 water. I do not know why water cannot be
recognized in the prmtop file.
I came with this solution to define water in the dyn.in
file: watnam='TIP3',OWTNM='OH2', hwtnm1='H1',hwtnm2='H2',
Then I am able to run the simulation.
Is this solution OK?
But I never have this problem using "old CHAMBER" to convert CHARMM
generated psf to prmtop and run in pmemd.cuda. Pmemd.cuda was always able
to recognize water molecules from "old Chamber" generated prmtop file.
Any comment?
Thanks!
On Tue, Apr 12, 2016 at 10:27 AM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>
> > On Apr 11, 2016, at 1:18 PM, Jun Feng <jufeng.mail.wvu.edu> wrote:
> >
> > Hi,
> >
> > I use the most recent CHARMM force field downloaded from Dr. Mackerell's
> > website named toppar_c36_feb16.tgz (a modified C36 protein parameter set)
> > to generate psf. I tried to use CHAMBER to convert to AMBER format
> prmtop.
> > But I get the following error message from CHAMBER:
> >
> > CMAP Found
> > Found 4 unique cmap types:
> > Type: 1 - 16 36 19 16 36 19 16 36
> > C NH1 CT1 C NH1 CT1 C NH1
> >
> > Type: 2 - 16 36 20 16 36 20 16 36
> > C NH1 CT2 C NH1 CT2 C NH1
> >
> > Type: 3 - 16 36 19 16 36 19 16 33
> > C NH1 CT1 C NH1 CT1 C N
> >
> > Type: 4 - 16 33 27 16 33 27 16 36
> > C N CP1 C N CP1 C NH1
> >
> > ERROR: CMAP reading terminated reading entry 19 / 576
> >
> > This might be incompatibility between the new c36 force field with
> modified
> > CMAP and CHAMBER. Can the CHAMBER developers provide some help to this
> > issue?
>
> The chamber program has been deprecated and removed from current versions
> of Amber. Try using the chamber action in ParmEd instead.
>
> Just make sure you get the latest version of AmberTools (15 currently)
> before trying it.
>
> You can find more details in the Amber 15 manual.
>
> You can also prepare your system in CHARMM-GUI, which will use ParmEd
> internally to create the appropriate Amber files for you.
>
> I know ParmEd has been used a decent amount with CHARMM 36, so unless your
> files are corrupted somehow, it should work.
>
> HTH,
> Jason
>
> > Thanks!
> >
> >
> > --
> > Jun Feng
> > Postdoc Fellow
> > Blake Mertz Research Group
> > Department of Chemistry
> > West Virginia University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jun Feng
Postdoc Fellow
Blake Mertz Research Group
Department of Chemistry
West Virginia University
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Received on Tue Apr 12 2016 - 12:00:03 PDT
