AMBER Archive (2008)

Subject: Re: AMBER: coordinate change of pdb structure using xleap

From: saurabh agrawal (imsam100_at_yahoo.co.in)
Date: Wed Aug 27 2008 - 02:23:09 CDT

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 Ă–berg <henrikob_at_kth.se> wrote:
From: Henrik Ă–berg <henrikob_at_kth.se>
Subject: AMBER: coordinate change of pdb structure using xleap
To: "amber_at_scripps.edu" <amber_at_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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