Dear Carlos,
Thanks for the reply. I am attaching the output of the dynamics part with
this mail. I would like to ask one more thing.
When i solvated another system which is a protein of 276 residues, I
notice that a lot of water molecules get into the interior regions of this
protein. to prevent it I used the optional closeness parameter of 2 or 3,
but with this I notice that a lot of regions of the water box r are
without the water molecules. can you please through some light on this
aspect also.
With regards,
Anshul Awasthi
Bioinformatics Center
Institute of Microbial Technology
Chandigarh, India.
Mobile +91-9872220352
On Mon, 19 Jul 2004, carlos wrote:
> please include the output for the MD part, it looks like your MD input
> might not be right at the part the specifies the restraints (or it could
> just be formatting change when you pasted into the mail).
>
> A rise in vdw energy is not uncommon for a TIP3P solvated system, the
> vdw energy of the water can be very high and is compensated by
> large negative electrostatics.
>
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Assistant 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
> ===================================================================
>
>
> &cntrl
>
> > imin=1,
> > maxcyc=15000, ncyc=4000, drms=0.001,
> > ntb=1, ntr=1,
> > cut=10,
> > ntpr=50,
> > &end Input for restraints (1-12) 10 RES 1 12 END
> >END
> >
> >
> >
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Received on Mon Jul 19 2004 - 18:53:01 PDT
