Re: [AMBER] Fwd: Desmond trajectory use with AMBER

From: <jojartb.jgypk.u-szeged.hu>
Date: Mon, 20 Oct 2014 06:15:39 +0200

Hi,
My suggestion is to prepare the topology and coordinate files with
amber, and thereafter you can use the amber_prm2cms.py script from
desmond distribution to create the cms file.
Afterwards run the simulation, use vmd to convert trajectory to dcd,
and you can use the parm7 file with the dcd to analyse trajectory.
HTH,
Balazs


Id├ęzet ("D.A. Ragland" <debra.ragland.gmail.com>):

> Greetings,
>
> I have been searching to find the answer to this question but I am afraid
> that my question is a bit more specific than the answers I've been able to
> find.
>
> Recently, my PI has made me switch to using Desmond to run simulations.
> Prior to the switch I was trained minimally on AMBER for simulations. I
> have a few AMBER specific perl scripts to measure Ca-Ca distances of
> trajectories (and RMSD, RMSF but I will not need these calculations) that I
> 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.
>
> 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



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Received on Sun Oct 19 2014 - 21:30:02 PDT
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