What does this mean "Cpptraj can read DCD files directly"? The scripts call
for top and crd files as well as the trajectory. Should I just change the
path to read the DCD file?
On Sunday, October 19, 2014, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sun, Oct 19, 2014 at 12:26 PM, D.A. Ragland <debra.ragland.gmail.com
> <javascript:;>> wrote:
> > would still like to use because they are familiar to me. I am aware that
> I
> > can load the Desmond trajectory into VMD to convert it into .top and .crd
> > files for use with AMBER, after converting the file to a DCD format.
> > However, I am not sure how to use the DCD file with my script (if this is
> > the trajectory file I am to use). I have attached the scripts for
> examining
> > if someone would be so kind.
>
> Cpptraj can read DCD files directly, so you shouldn't need to change
> anything. If you hit a snag let me know.
>
> -Dan
>
> > The "debptr" script is used to generate ptraj files. After these files
> are
> > generated, I used to load the appropriate trajectory file into the
> correct
> > folder and then submit the "nwptr" file to the cluster for analysis. Once
> > the ptraj analysis was complete I would then run the "atom distance"
> script
> > to determine specific Ca distance pairs. I am wondering if I should
> > generate the .top and .crd using the leap feature and then place the DCD
> > file into the appropriate folder so that I may use these scripts?
> >
> > I hope someone is able to help with this.
> >
> > Thank you.
> >
> > --
> > Debra Ragland
> > B.S. Chemistry
> > Ph.D. Candidate
> > UMass Medical School
> > Graduate School of Biomedical Sciences
> > Basic Biomedical Sciences Program
> > Schiffer Lab LRB 970M
> >
> >
> >
> >
> >
> > --
> > Debra Ragland
> > B.S. Chemistry
> > Ph.D. Candidate
> > UMass Medical School
> > Graduate School of Biomedical Sciences
> > Basic Biomedical Sciences Program
> > Schiffer Lab LRB 970M
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Debra Ragland
B.S. Chemistry
Ph.D. Candidate
UMass Medical School
Graduate School of Biomedical Sciences
Basic Biomedical Sciences Program
Schiffer Lab LRB 970M
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Received on Sun Oct 19 2014 - 12:00:03 PDT
