On Sun, Oct 19, 2014 at 12:53 PM, D.A. Ragland <debra.ragland.gmail.com> wrote:
> 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?
Yes. To be more specific, say previously you had an Amber NetCDF
trajectory and topology you read in like this:
parm mytopology.parm7
trajin mytraj.nc
The input for reading the DCD file is just this:
parm mytopology.parm7
trajin mytraj.dcd
-Dan
>
> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org <javascript:;>
>> 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
> _______________________________________________
> 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 - 12:30:03 PDT
