RE: Problems with energy minimization

From: Hongbo Du (hongbodu_at_uark.edu)
Date: Wed Apr 09 2014 - 10:17:08 CDT

Hi, James,

Please try to use packmol to construct your cells. At first, one cell including protein and water, another one including water, protein and ligand.

Good luck,

Hongbo
________________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of James Starlight [jmsstarlight_at_gmail.com]
Sent: Wednesday, April 09, 2014 9:38 AM
To: Namd Mailing List
Subject: Re: namd-l: Problems with energy minimization

Thanks for suggestion!

Its strange but I've tried to reconstruct this system in several ways ( using different initial conformations for docking as well as varying XYZ of system eventually obtaining the same effect.
but as I realize energy minimization is the actual way to resolve such clashes :) In any way could someone tell me

1- How it possible to found such clashes if visualization did not provide useful evidence.

2- Please provide me with some typical minimization.conf file (just for minimization of water-soluble system). How I could chose between stereed and CG-like algorithms ?

Thanks for help,

James

2014-04-09 18:14 GMT+04:00 Subbarao Kanchi <ksubbu85_at_gmail.com<mailto:ksubbu85_at_gmail.com>>:
Dear James,
                  It means that you have bad contacts in you initial structure. Reconstruct the initial system with out bad contacts.

Regards,
Subbarao Kanchi

On Wed, Apr 9, 2014 at 7:37 PM, James Starlight <jmsstarlight_at_gmail.com<mailto:jmsstarlight_at_gmail.com>> wrote:
Dear Namd Users!

I have problems of the simulation of my protein-ligand water-soluble system. First I've simulated apo form of my protein. Than I've took final conformation from that run and using autpdock I've placed ligand within the protein's interior re-solvable my system and run energy minimization. This minimization run produced errors like ( I've used such conf file for any other systems taking it from the Namd tutorial and have not any problems):

MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM DUE TO POOR PROGRESS
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
PRESSURE: 6 -nan -nan nan nan -nan nan nan -nan -nan
GPRESSURE: 6 -nan -nan -nan -nan -nan -nan -nan -nan -nan
ENERGY: 6 9999999999.9999 9999999999.9999 9999999999.9999 9999999999.9999 9999999999.9999 9999999999.9999 0.0000 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 1065900.0000 9999999999.9999 9999999999.9999

MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM DUE TO POOR PROGRESS
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan

I've tried to run it on gpu and cpu namd version but result was the same. How it could be fixed ?

Thanks for help,

James

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