Hi,
Please check that atom names are same in your input pdb (dock.pdb) and ligand.prepin files. While making prepin file some times it changes. If it is differing make them same.
I hope it will help.
Cheers,
Saurabh
--- On Wed, 27/8/08, Henrik Öberg <henrikob.kth.se> wrote:
From: Henrik Öberg <henrikob.kth.se>
Subject: AMBER: coordinate change of pdb structure using xleap
To: "amber.scripps.edu" <amber.scripps.edu>
Date: Wednesday, 27 August, 2008, 11:56 AM
Dear all,
I am using AMBER 9 simulating an enzyme docking during a 1 ns period. My
problem is not the actual simulation but the initial settings leading up to it.
When I load my ligand pdb file into leap, after using antechamber and parmchk,
through the following order:
source leaprc.gaff
loadamberprep ligand.prepin
loadamberparams ligand.frcmod
loadOff acn.off
loadamberparams frcmod.acn
DOCK=loadpdb dock.pdb
check DOCK (here I recieve some warnings but overall the unit is ok)
addions DOCK Na+ 0
DOCK2=copy DOCK
solvateoct DOCK2 ACNBOX 8.0
saveamberparm dock.prmtop dock.inpcrd
It is now I observe the problem. When I visualize the dock.inpcrd file the
ligand has changed coordinates, meaning the starting structure before minimizing
the system is not what I initially obtained from the docking program. Has anyone
encountered similar problems, or has anyone any suggestion?
Looking forward to replies!
Best regards
Henrik Oberg
KTH, Sweden
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Received on Sun Aug 31 2008 - 06:07:04 PDT
