Hi Tom
Thanks for your help.
I did check the restrt files that I made using Carnal and indeed, they
had "no" box information at the bottom of the file. Thus, as you
proposed I explicitly placed the box values (obtained from restrt files
printed out doing MD) into the ptraj script (imaging/converting to
pdb)and this did corrected the problem.
Thanks again for your help.
Steve
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On
> Behalf Of Thomas E. Cheatham, III
> Sent: Friday, July 30, 2004 4:42 PM
> To: amber.scripps.edu
> Subject: Re: AMBER: Imaging problem
>
>
> > I have a homodimer protein (each dimer has 99 residues), which
> > during my periodic box-simulations (explicit waters) separated. I
> > then tried Imaging using the following command:
> >
> > trajin wt.restrt_2500
> > trajout wt2500imaged pdb
> > center :1-99 origin
> > image :100-198 origin center
>
> image origin center
>
> is what you want here, but this doesn't explain the problem.
>
> > The dimers do reform, but the problem is that now there are hugh VDW
> > contacts between atoms. For example, I have an Oxygen from one
> > monomer
>
> > that is 1.97A to a Nitrogen of the other monomer.
>
> My guess is that the box information is not being read properly from
> the restart file and that the prmtop box information is overridding
it.
>
> Look at the last lines of the restart file where the box information
> is kept and explicity set this in the ptraj script, before the
> center/image commands, like below (exchanging the correct sizes).
>
> box x 45.900 y 35.00 z 50.00
>
> See if this works; in the meantime, I'll check to see if the box
> information is not being properly pulled out of the restart file.
>
> (note that if you read the trajectory, this problem should not occur,
> at least in my experience, and if it does, there is something funny
> going
> on...)
>
> --tom
>
> \ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy,
> Depts of
> | Medicinal Chemistry and of Pharmaceutics and Pharmaceutical
> Chemistry
> | Adjunct Asst Prof of Bioengineering; Center for High Performance
> | Computing University of Utah, 30 South 2000 East, Skaggs 201, Salt
> | Lake City, UT 84112
> |
> | tec3.utah.edu (801) 587-9652; FAX: (801)
> 585-9119
> \ BPRP295A / INSCC 418
> http://www.chpc.utah.edu/~cheatham
>
> ----------------------------------------------------------------------
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Received on Mon Aug 02 2004 - 21:53:00 PDT
