AMBER Archive (2009)

Subject: Re: [AMBER] broken Ligand

From: Shubhra Gupta (shubhg_at_iiar.res.in)
Date: Sat May 30 2009 - 01:35:46 CDT

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_at_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


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