[gmx-users] Re: Fwd: Ligand is moving far away after energy minimization

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 13 12:16:34 CET 2009

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Ms. Aswathy S wrote:
> Dept. Biotechnology
> Ext. 3108
> ----- Forwarded Message -----
> From: "Ms. Aswathy S" <aswathys at amritapuri.amrita.edu>
> To: "gmx-users" <gmx-users at gromacs.org>
> Sent: Thursday, March 12, 2009 8:19:42 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
> Subject: Ligand is moving far away after energy minimization
> Hi Justin,
> You were right. When I created the itp file using prodrg server, the coordinates of the drug has been changed. So that time itself it was away from the binding site.
> Now, instead of using the coordinate file from the prodrg, i have used the initial coordiantes of the drug for  minimization. But the grompp shows the follo: error.....
> Back Off! I just backed up STRA6/test_mdout.log to STRA6/#test_mdout.log.2#
> Getting Loaded...
> Reading file STRA6/test_b4em.tpr, VERSION 4.0.4 (single precision)
> Loaded with Money
> Back Off! I just backed up STRA6/test_em1.trr to STRA6/#test_em1.trr.2#
> Back Off! I just backed up STRA6/test_md.edr to STRA6/#test_md.edr.2#
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+01
>    Number of steps    =           50
> Step=    0, Dmax= 1.0e-02 nm, Epot=          nan Fmax= 1.81887e+12, atom= 4924
> -------------------------------------------------------
> Program mdrun, VERSION 4.0.4
> Source code file: nsgrid.c, line: 357
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
> Variable ci has value -2147483648. It should have been within [ 0 .. 17576 ]
> Is this the problem with the coordinates of the ligand? if so what should i do now?

There are two possibilities that immediately come to mind.

1. Bad steric clashing between elements of your system.
2. Improper parameters for some part of your system (most likely the ligand).

Visual inspection should aid if #1 is the case.  Literature reading and careful 
consideration should aid in #2.  Parameterization is tricky, and parameters from 
PRODRG almost always require manual adjustment and validation before they should 
be used.


> Thanks,
> Aswathy
>> Dear Gromacs users,
>> I am doing the MD of protein ligand complex. When I did the energy minimization of this complex,   in the result , the ligand molceule is moving far away from the protein.
>> What could be the possible reason? can anyone tell me how can i overcome this?
> Two possibilities come to my mind.
> 1. The parameters of the ligand are inappropriate, causing the ligand to be 
> ejected from the active site.  This is unlikely in a simple EM procedure, and 
> probably would cause lots of LINCS or "blowing up" warnings.
> 2. More likely: Your protein is positioned near a box edge and the ligand is 
> crossing periodic boundaries.  Consider how you set up the box and read about PBC:
> http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
> -Justin
>> Thanks in advance.
>> Aswathy
>> Amrita School of biotechnology
>> Dept. Biotechnology
>> Ext. 3108
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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