If you are trying to simulate protein with ligand and if you do not have co crystallized ligand protein sysytem then you need to draw the structure of the ligand in sybyl or maestro need to omtimize it and then dock this ligand in to your protein. You can use this system for further simulation study. As you know you just have to generate force field parameters for ligand using antechamber and prepin or librarary files using antechamber or leap. While generating topological parameters for whole system you need to load all frcmod and prepin files of ligand in tleap so tha it can recognize your ligand and then load your comlex system. All these steps are clearly mentioned in amber tutorial.
--- On Mon, 5/7/12, jit mukherjee <jitmukherjeechem.gmail.com> wrote:
From: jit mukherjee <jitmukherjeechem.gmail.com>
Subject: [AMBER] PLEASE GIVE SOME SUGGESTION
To: amber.ambermd.org
Date: Monday, May 7, 2012, 12:14 PM
If I want to simmulate an assembly by AMBER,part of which by AMBER
PARM99 force field and the other part by using ANTECHEMBER, then after
loading the part(by antechember) into xleap, how can I join that part
to the other part(by PARM99 force field) so as to build a single
UNIT,i.e., the whole assembly ? Please help me by giving your valuable
suggestions.
Thanking You,
With Regards,
jit mukherjee
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Received on Mon May 07 2012 - 21:30:05 PDT
