Absolutely--just change the ambmask and you should be fine. I would
suggest removing the restraints in stages: perform simulations on the 100ps
to 1ns scale as the restraints you wish to remove are reduced by perhaps a
factor of two or four until they get down to the 0.25 kcal/mol-A^2 range.
Just watch the restraint energy in the simulations and make sure it's not
changing too rapidly.
Dave
On Mon, Apr 11, 2016 at 2:02 AM, ABHIJEET CHOWDHURY <
f2013854.pilani.bits-pilani.ac.in> wrote:
> Dear Mr. Cerutti,
>
> If my previous refc file is created with some harmonic restraint on all
> residues but in my next simulation i want to restraint only few of the
> previous residues can I still opt for that file.
>
> Thank you.
>
> Regards,
> Abhijeet
> You will probably need that refc file; it looks like you know the input
> flag. This is the only way that sander / pmemd will know where the
> restraints should tie down. "Place a harmonic zero-length spring between
> this atom and this point (in the refc file)."
>
> The criteria for that file are that it have the same number of atoms as the
> system you are working with, nothing more. However, be very careful that
> the refc configuration makes sense and has good alignment to the rest of
> the structure. If, for instance, you take a refc that has the same
> configuration as your initial structure but translated 5A away in space,
> even though the reference file is a twin the restraint mask atoms are the
> only ones that will feel a strong impetus to shift their positions to
> realign with the refc structure. These sorts of shifts can sometimes
> happen during system setup.
>
> Cheers,
>
> Dave
>
>
> On Mon, Apr 11, 2016 at 12:11 AM, ABHIJEET CHOWDHURY <
> f2013854.pilani.bits-pilani.ac.in> wrote:
>
> > Dear Amber users,
> >
> > I am using group selection to restraint some residues with some harmonic
> > weight. Do I have to use -refc flag or should I leave it blank.
> >
> > And if I have to define some file for refc what is the criteria for
> > choosing that file (should it be from the just previous simulation or the
> > starting file with which I started the simulation)?
> >
> > Thank you.
> >
> > Regards,
> > Abhijeet Chowdhury
> > Student
> > M.Sc.(Hons.) Biological Sciences
> > B.E.(Hons.) Chemical Engineering
> > Birla Institute of Technology and Science (BITS),
> > Pilani 333 001, Rajasthan, INDIA
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 11 2016 - 06:00:05 PDT
