Dear Grant and Dan,
Thank you for the information. It worked. 🙂
Wu
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Friday, October 16, 2020 1:21 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd
On Fri, Oct 16, 2020 at 1:41 PM Grant Keller <Grant.L.Keller.80.nd.edu> wrote:
>
> Reading in netCDF files in VMD isn't supported in Windows. You can use
> cpptraj to output a copy of the trajectory in ASCII .crd format which
> should load in VMD just fine, something like cpptraj -p PRMTOP -y
> filename.mdcrd -x uncompressed.mdcrd. The default for unrecognized
> extensions like .mdcrd is the ASCII format.
You may also want to try converting to the charmm trajectory format
(e.g. '-x filename.dcd') since it is also a binary format (so no
precision loss and faster to process).
-Dan
>
> On Fri, Oct 16, 2020 at 12:23 AM Wu Xu <wu.xu.louisiana.edu> wrote:
>
> > Dear Amber users
> >
> > I used AMBER16 sander.MPI (-x filename.mdcrd) to create .mdcrd. However,
> > VMD 1.9.4 could not read it. So no frames were added into .prmtop loaded
> > first.
> >
> > I do not see the option "netCDF" format from VMD.
> >
> > Do you know how to solve this problem? Thanks,
> >
> > Wu
> >
> >
> > Dr. Wu Xu
> >
> > Professor of Biochemistry
> >
> > Department of Chemistry
> >
> > Room No. 138, Montgomery Hall
> >
> > 300 E. St. Mary BLVD
> >
> > P.O. Box 43700
> >
> > University of Louisiana at Lafayette
> >
> > Lafayette, LA 70504
> >
> > Telephone: 337-482-5684 (office)
> >
> > 337-482-6739 (lab)
> >
> > Fax: 337-482-5676
> >
> > Email: wxx6941.louisiana.edu<mailto:wxx6941.louisiana.edu>
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> AMBER.ambermd.org
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Received on Fri Oct 16 2020 - 20:00:02 PDT
