On Thu, Jan 26, 2017 at 6:54 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Yes, I have been saving velocities
Are you sure? Velocities are not saved by default. You have to set
ntwv > 0 or to -1 to combine with your coordinates trajectory (the
latter is for NetCDF only).
-Dan
>
> As I was using , ntx=5, irest=1,
>
> But I don't think I have velocity saved in any separate file.
>
> As in my script I just produce restrt, crd and out file.
>
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.edu>
> Sent: Thursday, January 26, 2017 12:34:33 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] How to make restrt file for specific step
>
> Had you been saving velocities to mdvel, you could have extracted the
> corresponding set of velocities and used it to create a restrt you could
> run from.
>
> Bill
>
>
> On 1/26/17 1:13 PM, Bill Ross wrote:
>> 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
>>>>> _______________________________________________
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>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe
>>> Laboratory of Computational Biology
>>> National Institutes of Health, NHLBI
>>> 5635 Fishers Ln, Rm T900
>>> Rockville MD, 20852
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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 Fri Jan 27 2017 - 10:30:03 PST
