Dear Sir,
The input file for ligand 1 and ligand 2 are named as lig.mol2 and
lig2.mol2 (In this, the bond between chlorine and carbon are intact)
After running the antichamber the out files are named as LIG.mol2 and
LIG2.mol2 respectively for lig.mol2 and lig2.mol2 using the following
command
command: ~/amber12/bin/antechamber -i lig.mol2 -fi mol2 -o LIG.mol2 -fo
mol2 -j 4 -at gaff -c AM1-BCC -nc 0
~/amber12/bin/parmchk -i LIG.mol2 -f mol2 -o LIG.frcmod
~/amber12/bin/antechamber -i lig.mol2 -fi mol2 -o LIG.mol2 -fo mol2 -j 4
-at gaff -c AM1-BCC -nc 0
~/amber12/bin/parmchk -i LIG.mol2 -f mol2 -o LIG.frcmod
Then tleap was run using the tleap script enclosed in attachment for
combining both ligands
Thanks & regards
*Dr. Ramesh M*
Faculty cum Scientist
Department of Medicinal Chemistry
National Institute of Pharmaceutical Education and Research (*NIPER*)
Rae bareli-229 010, Uttar Pradesh (UP), India
Post-Doctorate (Student no: 214585755; Staff No. 45951)
Department of Medicinal Chemistry
Discipline of Pharmaceutical Sciences, School/College of Health Sciences
University of KwaZulu-Natal (*UKZN*), Durban-4001, South Africa
The Editor
Innovations in Pharmaceuticals & Pharmacotherapy (*IPP*)
(Peer Reviewed International Journal)
http://innpharmacotherapy.com/EditorialBoard.aspx
Email: shreeramesh.gmail.com
Mobile: 91 + (0) 9646469938 27+ (0) 844556164
On Fri, Feb 20, 2015 at 7:48 AM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> > On Feb 20, 2015, at 10:40 AM, David A Case <case.biomaps.rutgers.edu>
> wrote:
> >
> > On Fri, Feb 20, 2015, Jason Swails wrote:
> >>
> >> In the OP's defense, if he is using Mac OS X, his filesystem is likely
> >> case-insensitive, so this should work.
> >
> > It won't work: He(she) loaded a mol2 file with Tripos atom types, then
> > did "saveamberparm". Hard to beleive that this did not emit all kinds of
> > fatal errors....
>
> Oh, of course; antechamber would write out a mol2 with gaff atom types.
>
> Thanks,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Sat Feb 21 2015 - 08:00:03 PST
