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
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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Apr 10 2016 - 23:30:04 PDT
