So I break my promise to wait. Below is pytraj solution.
You need to create a file (e.g myscript.py) then copy my code to your file.
then
python myscript.py
https://github.com/hainm/amber_things/issues/18
let me know if that helps.
Hai
On Thu, Jun 16, 2016 at 1:07 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> So you mean loading forces with given parm file and then striping water,
> then writing to a new trajectory?
>
> If yes, I think I can have a solution for you with pytraj.
>
> But I will wait until Dan or other give you solution with cpptraj first.
>
> Hai
>
>
> On Thu, Jun 16, 2016 at 12:53 PM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
> wrote:
>
>> Thank you for prompt response and suggestion.
>>
>> I have saved separate coordinate, velocity and force trajectories created
>> using below command options with PMEMD.
>> -x ${TRAJDIR}/sys.mdcrd.nc \
>> -v ${TRAJDIR}/sys.mdvel.nc \
>> -frc ${TRAJDIR}/sys.mdfrc.nc
>>
>> This way I have a coord file, a mdvel file and a force file.
>>
>> 1. I want to strip out force values from force trajectory as you
>> suggested,
>> but for that I need to have a trajectory which contains coords as well as
>> force values.
>>
>> 2. "trajout out.nc force" does use of force option asks cpptraj to output
>> only force part of the trajectory? or it outputs coords & force?
>>
>> 3. Is there any way to load only force values not coordinates with the
>> corresponding .prmtop file?
>> if not then, how to separate coordinated and force trajectory after
>> stripping solvents
>>
>> May be I did not got it right, but I tried to look into source code of
>> cpptraj packaged with AmberTools16 and searched for keyword mdfrc and
>> found
>>
>> Trajin_Single.cpp
>> 80: // TODO add in support for separate mdfrc file
>> 97: // TODO open mdfrc file if present
>> 106: // TODO close mdfrc file if present
>> 160: // TODO open mdfrc file if present
>> 180: // TODO close mdfrc file if present
>>
>> A similar thread related to mdvel file reading:
>> http://archive.ambermd.org/201605/0225.html
>>
>> suggests use of mdvel keywork with trajin, so I thought that there may be
>> mdfrc keyword as well and searched for it in source code, because it was
>> mentioned that mdvel option is not documented in manual
>>
>>
>>
>> On Thu, Jun 16, 2016 at 8:24 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>>
>> > do you mean writing coordinates with force?
>> >
>> > If yes, this is example with *cpptraj*
>> >
>> > parm systemVF.parm7
>> > trajin systemVF.nc
>> > strip :WAT
>> > trajout out.nc force
>> >
>> > pytraj does not support that yet.
>> >
>> > Hai
>> >
>> > On Thu, Jun 16, 2016 at 9:33 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in
>> >
>> > wrote:
>> >
>> > > Dear Amber user,
>> > >
>> > > Are there any ways to read and after striping solvent write out mdfrc
>> > > trajectory netcdf files generated by pmemd using cpptraj or pytraj.
>> > >
>> > > Thank you
>> > > _______________________________________________
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>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
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>> >
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Received on Thu Jun 16 2016 - 11:00:02 PDT
