AMBER Archive (2008)

Subject: Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jun 02 2008 - 15:06:39 CDT

take a look at the ptraj part of the manual- what it wants after the ptraj
exe is the name of the prmtop. you gave it trajin, so it thinks that is
a file it should load. the trajin is a command to be given later.
it might help to go through the tutorials, I think the DNA one gives some
nice sample ptraj scripts that will be a better place to start.
good luck
carlos

On Mon, Jun 2, 2008 at 3:54 PM, Campbell, Patrick <pcampbell_at_msm.edu> wrote:
> Hello Dr. Simmerling,
>
> Here is the ptraj script for the mdcrd file as requested.
>
>
>> $AMBERHOME/exe/ptraj trajin 1nsMD_040408.mdcrd
>
> When I am attempting this command now however, I am getting a
> different error message and not the one that I previously sent to you.
>
>
> Amber8 Module: ptraj
> Could not open file (trajin) with mode (r)
> ERROR in ptrajInitializeState(): Attempting to open parameter/topology file
> trajin
>
> Suggestions will be warmly appreciated.
> Pat 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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