AMBER Archive (2003)

Subject: Re: Protein - DNA complex simulation - protocol

From: Harikrishnan (harikrism_at_yahoo.co.in)
Date: Tue Apr 29 2003 - 08:16:25 CDT

Hi,

Sorry for not giving details in my previous mail.
I started with coordinates of protein and dna from PDB
with modifications and then added water and ions, in
that order, using xleap. Then 1000 steps SD
minimization with only water allowed to move (ntr
=1)followed by four 100 steps SD where the restraints
on ions were removed faster than that on dna and
protein. Finally 1000 steps SD was done on the system
without restraints.

This was followed by MD where the ions, dna and
protein were kept harmonically restrained for 25 ps
and at the same time the temperature was increased
gradually to 300K. This was followed by four MD (5 ps
each) with removing the restarints (from 25 kcal to
nil)on dna and protein slowly and ions fastly. Then I
did about 10ps MD before moving on to actual
production run.

All MD simulations were with PME on and at constant
pressure.

After about 300 ps I got SHAKE problem. In fact the
water molecules started moving out just as the
equilibration started and the box got deformed.

Expecting some good protocol for protein -dna
simulation from experts..

thanks
Hari

 --- Andreas Svrcek-Seiler <svrci_at_tbi.univie.ac.at>
wrote: > Hi,
> >
> > I feel that there is some problem with my
> > equilibration protocol.
> It would be helpful to describe your protocol, so
> that others could see what might have gone wrong.
>
> regards
> Andreas
>
> --
>

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