You will need to re-equilibrate to generate velocities.
Bill
On 1/26/17 12:57 PM, Thakur, Abhishek wrote:
> Hi
>
> It worked with .rst7 extension.
>
>
> But when I am putting that restrt file for aMD it is complaining could not find much information about velocity in the restrt
>
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Thursday, January 26, 2017 9:30:16 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] How to make restrt file for specific step
>
> 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
>>> _______________________________________________
>>> AMBER mailing list
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>>>
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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://urldefense.proofpoint.com/v2/url?u=https-3A__www.lobos.nih.gov_lcb&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=a6auFNIIlYHTuNiYRR-DXyBBrwH-hqDW_xQCi_ldegU&s=M9MSzUUL6VOGgQ9v4UDx_ROU_2IjtALtASGZ5kxRppk&e=
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Received on Thu Jan 26 2017 - 13:30:02 PST
