AMBER Archive (2008)

Subject: AMBER: coordinate change of pdb structure using xleap

From: Henrik Öberg (
Date: Wed Aug 27 2008 - 01:26:42 CDT

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
loadamberparams frcmod.acn
DOCK=loadpdb dock.pdb
check DOCK (here I recieve some warnings but overall the unit is ok)
addions DOCK Na+ 0
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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