To just minimize hydrogens while restraining the heavy atoms you can
set ntr=1 (make sure you specify reference coords on the command line
with -ref) and set restraintmask = ':X-Y & !.H=' where X and Y are the
starting and ending residue numbers of what you want restrained. To
gradually relax the restraints the easiest way is to start with a
reasonably high restraint_wt (I usually use around 5.0 kcal/mol A^2 or
so), then restart the run with smaller and smaller restraint_wt
values. See the "Frozen or restrained atoms" section of the Amber
manual (section 2.6.4) for more information.
-Dan
On Mon, Oct 4, 2010 at 3:11 AM, abc def <biotechabc.gmail.com> wrote:
> Hi all,
>
> Actually I want to do the minimization of DNA complex by first subjecting
> the complex to Hydrogen minimization that were added explicitly by using
> tleap followed by restraint minimization of the DNA and counterions. And I
> want to gradually relieve the restraint on DNA and counterions.
>
> Now the problem is that I dont know to how to go about this. I found a post
> in the archive where the same question has been asked in 2002. But I
> couldn't find the answer to that.
>
> Can you please tell me that for minimizing hydrogens what should I specify
> keeping the DNA and ligand intact?
>
> Hoping for an early reply.
>
> Thanks in anticipation.
>
> Regards,
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Oct 04 2010 - 05:30:04 PDT
