AMBER Archive (2005)

Subject: Re: AMBER: rst file problems

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Tue Apr 12 2005 - 15:39:35 CDT

Mathew-

I played around with a system like this a couple of years ago--kept
crystallographic waters around my protein but ran non-periodic with gB for
solvation, trying to get the best of both worlds. I found that 1 kcal harmonic
positional restraints (ntr=1) on the oxygen atoms of the waters was enough to
keep them from flying away. Just restraining the oxygen allowed the waters to
reorient and interact w/protein. Kind of interesting, but I ended up going with
a full explicit periodic simulation instead. Guess it depends on your research
question.

Good luck!
Kristina

Quoting Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>:

> using explicit solvent mixed with continuum models can be difficult
> and is still a research problem. you might want to try restraints, or else
> remove these waters. in any case you can't let them float away, it will
> cause
> problems like what you've seen with the coordinates getting
> too large.
>
> mathew k varghese wrote:
>
> >Dear simmerling,
> >
> >Thanks for your help.
> >Yes, my system contains crystallographic waters which
> >fly off into large distances as the temperature
> >increases from 0K to 300K. Even when the temperature
> >is fixed at 300K the water molecules fly off. How can
> >I deal with this problem. Should I impose some
> >restraints on the water molecules? If so how can I do
> >that.
> >thanking you,
> >
> >--- Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
> >wrote:
> >
> >
> >>you can't just delete data form the restart file,
> >>then the
> >>coordinates won't be given to the right atoms.
> >>you need to solve the problem of the asterisks.
> >>
> >>it looks like some of your coordinates are larger
> >>than
> >>1000 angstroms, while others are much smaller.
> >>did the MD that produced this file complete without
> >>anything unusual, or any large energies?
> >>is the system very large? is it more than 1
> >>molecule? maybe
> >>they have become separated very far in space.
> >>you'll need to look at your system and find out what
> >>is
> >>happening to the structure to cause such large
> >>coordinates.
> >>
> >>
>
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Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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