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
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Received on Sun Oct 19 2014 - 12:30:04 PDT
