From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Wed Apr 09 2014 - 09:14:55 CDT
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
>
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:18 CST