AMBER Archive (2008)

Subject: Re: AMBER: Need help... High energies for complex...

From: Carlos Simmerling (
Date: Thu Sep 04 2008 - 10:41:38 CDT

are the coordinates you are using for the complex exactly the same as
for the protein and sugar alone (the energies you posted earlier)?
if not, then you really can't use this to debug your energies. they
must be identical (but separate files).
if yes, then there is something wrong in the prmtop files and you will
need to go through your procedure for generating the separate files
and make sure they are the same.
all of this assumes no covalent link between sugar and protein.

On Thu, Sep 4, 2008 at 11:22 AM, Waqas Nasir <> wrote:
> Hi,
> Well, thanks a lot for the worthed help.
> Let me explain the whole procedure that I have taken up, I have some doubts
> in the way I have separated the files and the first thing that came into my
> mind after these results was exactly that the top files are not
> corresponding to what is in the results.
> Anyways, the sugar that I have is a tetra saccharide. I first constructed
> the sugar unit in xleap and added 3 bonds which were missing when I
> imported the pdb file into the xleap with glycam_06 force field (The reason
> being not able to find the exact residues in the glycam06 force field as are
> in the pdb file). Along side that I had a protein unit from the part of the
> pdb file which contained protein. I combined both units in xleap by combine
> command and then generated the prmtop and inpcrd files for the main complex
> on which I had all the minimization and md runs going on.
> Secondly the script for generating frames generated 250 pdb files
> corresponding to the 250 frames that I had in the trajectory. I again
> repeated the same procedure using tleap and constructed a sugar subunit and
> a protein subunit for each frame and generated top and crd files separately
> for the two subunits in each frame. These files were then used for
> subsequent single point energy calculations.
> Do you see mistakes in principle of the approach that has been taken up
> here???
> Awaiting your response,
> Thanks a lot,
> Waqas.
> ----- Original Message ----
> From: David A. Case <>
> To:
> Sent: Thursday, September 4, 2008 5:36:37 PM
> Subject: Re: AMBER: Need help... High energies for complex...
> On Thu, Sep 04, 2008, Waqas Nasir wrote:
>> Well, I have tried straight single point md on the complex,sugar and
>> protein
>> separately, and what I have found is as follows;
> This is not what you should do, at least until you understand what is
> going on. My suggestion (and Carlos'):
> Make a single prmtop file for the complex. Use this prmtop file for
> a single point calculation with two sets of coordinates: one with the ligand
> (sugar) in its binding location, and a second set of coordinates where you
> manually move the ligand to someplace distant from the protein, (but keep
> the
> protein coordinates identical to what they were in the complex.
> Once you see and understand how that works, you will be ready to try and
> interpret other experiments.
> ...regards...dac
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Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
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Stony Brook University E-mail:
Stony Brook, NY 11794-5115 Web:
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