AMBER Archive (2002)

Subject: Re: Can we get trajectories coordinates after FIT in Carnal? (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Mon Aug 26 2002 - 16:51:03 CDT

---------- Forwarded message ----------
Date: Wed, 14 Aug 2002 17:48:03 -0400
From: Carlos Simmerling <carlos.simmerling_at_sunysb.edu>
To: William Wei <william_at_phm.utoronto.ca>,
     Amber List <amber_at_heimdal.compchem.ucsf.edu>
Subject: Re: Can we get trajectories coordinates after FIT in Carnal?

I would think that ptraj would be the module to use for this.
Carlos

----- Original Message -----
From: "William Wei" <william_at_phm.utoronto.ca>
To: "Amber List" <amber_at_heimdal.compchem.ucsf.edu>
Sent: Wednesday, August 14, 2002 5:52 PM
Subject: Can we get trajectories coordinates after FIT in Carnal?

> Hi, Good afternoon, my purpose is get the snapshots from my dynamics
> simulation using carnal. Can carnal do that? I tried to get it, but I
> failed. Here is my input file for carnal. Can anybody help me to figure it
> out? Thanks.
>
> William.
> -------------------
> FILES_IN
> # Input the parm.top file, and the coordinates.
> PARM p1 CMVDimer.top;
> STREAM s1 CnsP_51.2_90.6psR_mdcrd.Z
> CnsP2.5_3nsR_mdcrd.Z;
> STATIC ref1 CMVDimer.crd;
>
> FILES_OUT
> COORD c1 DimerTrj.pdb PDB;
>
> DECLARE
> GROUP g1 (((RES 209-222, 457-470))&(ATOM TYPE CA));
>
> RMS rms1 FIT g1 s1 ref1;
>
> OUTPUT
> COORD c1 s1 MOD 10 ATOM 8328;
>
> END
>
>
> -------------------------
> William Wei
> Faculty of Pharmacy
> 19 Russell Street
> Toronto, ON. M5S 2S2
> Tel: 1-416-946-8469
> Fax: 1-416-978-8511
> Email: william_at_phm.utoronto.ca
> william.wei_at_utoronto.ca
>
>
>
>