I have tried
trajin PRMT7_WT_avg_160ns.crd.gz 739 739
trajout PRMT7_WT_avg_160ns_739.rst
trajout PRMT7_WT_avg_160ns_739.pdb
and it can form the desired pdb.
But just I am not gaining confident because I am unable to generate pdb from this file restrt file PRMT7_WT_avg_160ns_739.rst
To put it as input for my aMD
________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: Thursday, January 26, 2017 9:13:10 AM
To: AMBER Mailing List
Subject: Re: [AMBER] How to make restrt file for specific step
> 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
You could try outputting a pdb instead of rst from cpptraj, and see what
it contains.
Bill
On 1/26/17 12:08 PM, Thakur, Abhishek wrote:
> 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 - 12:30:04 PST
