Hi Sergio,
I also use restraints. But it seems like the reference structure is scaled along
with the simulated structure.
I use only 5kcal/(mol*A) ... on protein and ligand. This is per atoms afaik and
holds the restrained molecules very stron in their initial position in all other
cases.
I also tried playing with the pressure coupling constant taup and tried to get
higher initial density by lowering the closeness parameter in LEaP and the size
of the solven shell ... without real success.
Cheers,
Alexander
________________________________
Von: Sergio R Aragon <aragons.sfsu.edu>
An: AMBER Mailing List <amber.ambermd.org>
Gesendet: Freitag, den 10. September 2010, 19:26:41 Uhr
Betreff: Re: [AMBER] Complex distorts during pressure adjustment in
equilibration
Hello Alexander,
I normally use a restraint parameter of 500 when the intent is to keep the
protein from moving. What parameter do you use? Can you increase it? The
other thing to make sure of is that the number of residues to hold fixed does
include the ligand portion of your molecule. Could it be that you are not
fixing the atoms of the ligand and only the protein?
Cheers, Sergio
-----Original Message-----
From: Alexander Metz [mailto:alexander_metz2000.yahoo.de]
Sent: Friday, September 10, 2010 3:41 AM
To: amber.ambermd.org
Subject: [AMBER] Complex distorts during pressure adjustment in equilibration
Hello,
I am currently equilibrating a system for MD like many times before. The problem
is that during the NTP pressure adjustment step my complex gets distorted. This
is due to the distance rescaling. It has not been a big deal for globular
proteins with the ligand rather close to the center of the solvent box since the
rearrangement of the complex was minimal.
But the system I want to study is rather elongated. I use a rectangular box
(~130x40x40A). Also the initial density is rather low after solvating with LEaP
(~0.8g/ml). The ligand resides at one end of the elongated protein.
This results in the ligand shifting significantly (>2A) with respect to the
protein during the density adjustment. Also the 2 parallel helices in the
dimeric protein shifts significantly. This happens depsite of using positional
restraints.
In general I think that only the water should adjust so that that solute stays
in its original configuration. But unfortunately the positions of all molecular
entities are rescaled.
Is there an easy way to prevent this?
Best regards,
Alexander
++++++++++++++++++++++++++++++++++++++++++++++++++
Alexander Metz (PhD Student)
Heinrich Heine UniversitätDüsseldorf
InstitutfürPharmazeutischeundMedizinischeChemie
Computational Pharmaceutical Chemistry
Universitaetsstrasse 1
40225 Düsseldorf, Germany
Tel: +49 211 81 13854
++++++++++++++++++++++++++++++++++++++++++++++++++
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Received on Fri Sep 10 2010 - 11:30:05 PDT
