Dear Jason;
Say I extract the trajectory with frames below RMSD 1 Ang. from the
reference structure using this
trajin *md1.mdcrd*
rms R1 first :1-198 .CA
outtraj frames_rms1_md1.mdcrd maxmin R1 min 0.0 max 1.0
Say now I have frames_rms1_md1.mdcrd. How can I process this
frames_rms1_md1.mdcrd file for MMGBSA/MMPBSA and how can I define frames in
this case. Also frames_rms1_md1.mdcrd contins trimmed trajectories within
RMSD 1 Ang.. So if I want to process this trajectory how can I process it
for mmpbsa or gbsa. How an input file will look like in this case.
Thank you so much for all your time and help.
On Mon, Jun 23, 2014 at 8:49 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Mon, 2014-06-23 at 16:45 +0200, Soumendranath Bhakat wrote:
> > Dear Dan;
> >
> > Say I want to calculate both GBSA and PBSA calculations on these filtered
> > frames. How the script should be and how can I know which is starting
> frame
> > and which is end frame?
>
> The start frame and end frame correspond to the frame numbers of the
> input trajectories (frames are numbered from 1 to N in the order that
> the trajectories are specified in).
>
> > Below a prototype script to run parallel PBSA and GBSA. How can I know
> > frame numbers that will be filtered?
>
> The input file below will use frames 1 through 50, inclusive. The
> filtering variables are: startframe, endframe, interval. The frames
> analyzed will be startframe, startframe+interval, startframe
> +2*interval, ..., startframe+N*interval for all frames less than or
> equal to endframe.
>
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Mon Jun 23 2014 - 12:30:03 PDT
