It looks like mdcrd file was messed up during running ptraj program.
Because the distance between one backbone C and one water O is only 0.89
A. But some water molecules look fine, just as the restart file. My
guess would be the "image" water molecules are wrong positioned. Maybe I
should image water then run rms to fit protein.
reference ycd.inpcrd
trajin md_npt2.crd.gz
rms reference out rms-ycd-cry-320k .CA
center .CA
image center
strip ~:1-316,1091,5345,5702,5902,6376,8799,9524,10065,12061,12382,15338
trajout md_npt2_waterpath.crd
go
On Thu, 2005-10-27 at 15:40, Mingfeng Yang wrote:
> The easiest way and the most trustable way is look at both files.
> See if the last serveral coordinations in your mdcrd file match the
> corresponding coordinations in your restart file.
>
> Mingfeng
>
> Lishan Yao wrote:
>
> >But the total steps are 500,000. The last snapshot should be the same as
> >restart, right?
> >
> >Lishan
> >
> >On Thu, 2005-10-27 at 15:03, Carlos Simmerling wrote:
> >
> >
> >>if you write the traj file every 1000 steps and restarts every 100 steps,
> >>they will not match.
> >>
> >>===================================================================
> >>Carlos L. Simmerling, Ph.D.
> >>Associate Professor Phone: (631) 632-1336
> >>Center for Structural Biology Fax: (631) 632-1555
> >>Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> >>Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
> >>===================================================================
> >>
> >>
> >>
> >>
> >>Lishan Yao wrote:
> >>
> >>
> >>
> >>>The simulation finishes normally. The restart file was written out by
> >>>default, every 100 steps.
> >>>
> >>>Best,
> >>>Lishan
> >>>
> >>>On Thu, 2005-10-27 at 12:18, Carlos Simmerling wrote:
> >>>
> >>>
> >>>
> >>>
> >>>>did the simulation finish normally? how often did you write
> >>>>restarts?
> >>>>
> >>>>===================================================================
> >>>>Carlos L. Simmerling, Ph.D.
> >>>>Associate Professor Phone: (631) 632-1336
> >>>>Center for Structural Biology Fax: (631) 632-1555
> >>>>Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> >>>>Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
> >>>>===================================================================
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>Lishan Yao wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>Dear Amber users:
> >>>>> I did a 500,000 steps MD simulation and I saved snapshots every 1000
> >>>>>steps. My question is whether the restart file and the last snapshot in
> >>>>>crd (trajectory) file has the same structure? The reason I ask this
> >>>>>question is that I found out water molecules in active site have
> >>>>>different positions in the two structures.
> >>>>>
> >>>>> Thank you in advance.
> >>>>>
> >>>>>Best,
> >>>>>Lishan
> >>>>>
> >>>>>
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Received on Thu Oct 27 2005 - 21:53:00 PDT
