On Wed, Oct 12, 2011 at 2:05 PM, kirtana S <skirtana4.gmail.com> wrote:
> I am to perform REMD on 50 mer polymer , I was going through the tutorial
> 7
> .
> The makeCHIR_rst , is this specifically for the peptide .
> Is there way of generating the chiral restraints for this polymer chain.
>
Does the polymer need chiral constraints (i.e. is it chiral)? If so, you
have to figure out which 4 atoms define the chiral constraints and then
modify makeCHIR_RST to include your polymer residues in the definition
file. Note that makeCHIR_RST is just a shell script, so you can edit it.
Use the existing amino acids present in the definition file as examples of
how to do this.
HTH,
Jason
> Thanks
> kirtana
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 12 2011 - 18:00:03 PDT
