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

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 26 Jan 2017 15:30:16 -0500

On Thu, Jan 26, 2017 at 3:08 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>
> trajin WT_avg_160ns.crd.gz 739 739
> trajout WT_avg_160ns_739.rst

Note that cpptraj does not recognize '.rst' as an Amber restart
extension - you are likely writing WT_avg_160ns_739.rst as an Amber
ASCII trajectory (to know for certain check the output from cpptraj -
it will tell you what format it is using for the output trajectory).

Either use the extension '.rst7' or add the 'restart' keyword to your
'trajout' line.

-Dan

>
> ./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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-- 
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Jan 26 2017 - 13:00:02 PST
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