Hi,
Previously you said:
> 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
I'm saying that since cpptraj can read a DCD file you shouldn't need
to change anything in your script once you have the DCD file. Just use
the DCD file where you previously used an Amber trajectory file. So
your procedure would be:
1. Desmond traj -> VMD -> DCD traj
2. DCD traj -> CPPTRAJ -> Analysis
The topology you use can be whatever format CPPTRAJ understands (Amber
Top, Charmm PSF, CIF, PDB, Mol2, etc).
-Dan
On Sun, Oct 19, 2014 at 1:09 PM, D.A. Ragland <debra.ragland.gmail.com> wrote:
> I'm sorry I don't follow, where do I generate the topology file ? Or how
> from a desmond simulation? Or do I generate the .top file from the starting
> pdb using the leap feature ?
>
> On Sunday, October 19, 2014, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> On Sun, Oct 19, 2014 at 12:53 PM, D.A. Ragland <debra.ragland.gmail.com
>> <javascript:;>> 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
>> <javascript:;>> wrote:
>> >
>> >> Hi,
>> >>
>> >> On Sun, Oct 19, 2014 at 12:26 PM, D.A. Ragland <debra.ragland.gmail.com
>> <javascript:;>
>> >> <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:;> <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:;> <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 <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 - 12:30:04 PDT
