Re: Problems with energy minimization

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Wed Apr 09 2014 - 09:38:21 CDT

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>:

> 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>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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