AMBER Archive (2004)

Subject: Re: AMBER: Bad contacts

From: Carlos Simmerling (
Date: Mon Jun 07 2004 - 20:26:19 CDT

the minimization output of sander will list the atom
with the largest force, maybe that will be a starting point
to try to identify the bad contact or other structure problem.
2175 kcal/mol is indeed a very high energy.

----- Original Message -----
From: <>
To: <>
Sent: Monday, June 07, 2004 8:44 PM
Subject: AMBER: Bad contacts

> Hello, Amber:
> I built a protein model from the homology crystal structure using
> Swiss-3D modeling program. Hydrogen atoms were added to this model in
> tleap. And the model was subjected to sander (Amber7) energy
> minimization under non-periodic boundary condition. The idea is to have
> a simple run for the entire molecular system. It went through.
> The total energy level was lowered from '2.1754E+03' to '-3.1382E+03';
> RMS was lowered from '2.1393E+02' to '4.4849E+00'; VDWAALS was lowered
> from '4159.9961' to '-827.5665'.
> My input file for sander run is :
> 'initial minimization test 1d
> &cntrl
> ntb=0, imin=1, maxcyc=200, ntpr=5
> &end'
> Then I checked the structures of before and after energy minimization
> using SwissPDB Viewer. For the initial structure, no bad contact was
> found for either 'aa making clashes' or 'aa making backbone clashes'.
> For the structure after minimization, several residues are identified in
> making clashes and making backbone clashes. I notice that there are some
> complaints when I loaded the minimized structure in SwissPDB Viewer, such
> as 'some hydrogen atoms could not be connected', 'atoms of unknown group
> have been treated as HETATM. Numbers of groups treated as HETATM (5)',
> and ''at least one HETATM group lacked proper CONNECT information,
> connections will be generated between atoms that are closer than 2.000A,
> which can generate false bonds. Nb of HETATM groups in this case (10)'.
> My questions are:
> (1) The bad contacts in structural (after minimization) are caused by
> <a> the program incompatibility between Amber and SwissPDB Viewer? Such
> as HIS in SwissPDB Viewer while HID in Amber. When loading pdb file in
> tleap, Amber automatically add the missing atoms to the file. These atoms
> may be the trouble fro SwissPDB Viewer to recognize?: or by
> <b> the different on force field definition between SwissPDB Viewer and
> Amber7. When I ran tleap (Amber7), I used .ff99 for loading .pdb files.
> (2) Are there any improper setting in my input file for sander run? If
> so, is this the reason for these bad contacts? If not, how energy
> minimization create some bad contacts? While it suppose to improve the
> structure modeling as I understand.
> I am bit of confused on which structure model should be used. Your help
> and advice will be much appreciated.
> Thank you
> Bo Yang
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