Dear Prof. Case:
Sorry for sparse information. I have attached the files. a.pdb file I got
after saving topology (a.prmtop) and parameters (a.inpcrd). I Sourced
leaprc.GLYCAM_06 and leaprc.gaff. For solvation I used TIP3PBOX and 7.0
buffer. min.in was input file to execute sander for minimization. Resulted
a_min.pdb is after minimization, where the ligand is broken.
Thanking You,
Shubhra
On Fri, May 29, 2009 at 7:45 PM, David A. Case <case.biomaps.rutgers.edu>wrote:
> On Fri, May 29, 2009, Shubhra Gupta wrote:
> >
> > I am using Amber 10. After minimization most of the ligands
> > have been broken. Can anybody help me this regard.
>
> Please ask yourself: "Is is possible that anyone could help, given such
> sparse
> information?"
>
> ...dac
>
>
- application/octet-stream attachment: a.prmtop
- application/octet-stream attachment: a.inpcrd
- application/octet-stream attachment: min.in
- chemical/x-pdb attachment: a.pdb
Received on Sat May 30 2009 - 01:16:40 PDT
