Re: [AMBER] How to make restrt file for specific step

From: Thakur, Abhishek <axt651.miami.edu>
Date: Thu, 26 Jan 2017 20:08:26 +0000

Hi Hai

I have tried by making a ex.trajin file

trajin WT_avg_160ns.crd.gz 739 739
trajout WT_avg_160ns_739.rst

./cpptraj -p WT.prmtop <ex.trajin> ex.out

it forms restrt file but gives me an error when I try to make pdb file from rst file and check istructure.
Ambpdb complains that atoms number does not match with prmtop file


________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Thursday, January 26, 2017 8:56:29 AM
To: AMBER Mailing List
Subject: Re: [AMBER] How to make restrt file for specific step

Please see trajout command in cpptraj.

(probably you just need

parm your.parm7
trajin your.nc 5000 5000 # just an example of your desired frame
trajout your.rst7
)

Hai

On Thu, Jan 26, 2017 at 2:52 PM, Thakur, Abhishek <axt651.miami.edu> wrote:

> Hi everyone,
>
>
> I am doing aMD so after 10ns of production run I have extracted the lowest
> energy structure at around 50steps.
>
> Can any one help me out, how to create restrt file for that particular
> step of MD.
>
>
>
>
> Thanking you,
>
> Abhishek
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Received on Thu Jan 26 2017 - 12:30:02 PST