Hi,
On Sun, Oct 19, 2014 at 12:26 PM, D.A. Ragland <debra.ragland.gmail.com> 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
> 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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Received on Sun Oct 19 2014 - 12:00:02 PDT
