AMBER Archive (2009)

Subject: Re: [AMBER] Error running MM _PBSA.pl script

From: liuhui (fredliu1_at_sohu.com)
Date: Tue May 19 2009 - 09:29:23 CDT

Dear Vikas Sharma,
  The output file suggests that you still have a problem with the
'fillratio' parameter. It is said that "fillratio = 4.0" has been added,
however, I guess that you didn't put it in place. It should be added in the
"&pb" namelist, not "&cntrl".
  The "fillratio" problem has been mentioned so many times in the
mailing-list, maybe that parameter for a small molecule PB caculation could
be added in the mmpbsa.pl of AMBER11.

regards,

Hui Liu
Dept. of Biochemistry and Molecular Biology
College of Life Sciences
Wuhan University
Wuhan, China

--------------------------------------------------
From: "Vikas Sharma" <vs_vikassharma_at_yahoo.co.in>
Sent: Tuesday, May 19, 2009 12:34 PM
To: "AMBER Mailing List" <amber_at_ambermd.org>
Subject: Re: [AMBER] Error running MM _PBSA.pl script

> Dear Dr. Ray Luo,
> Thanks for the reply..
> i have pasted the file at end of this mail...
> i had the same error and one of the users told me to add "fillratio = 4.0"
> to my binding_energy.mmpbsa ...i did that and again i got the same
> error...
>
> how can i resolve this error?
>
> thanks
>
>
>
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> NB-update: residue-based nb list 654
> NB-update: atom-based nb list 773
>
>
> ======== Setting up Grid Parameters
> ========
> Using bounding box for grid setup
> Bounding Box Center: 26.500 52.000 29.500
> Xmin, Xmax, Xmax-Xmin: 21.866 30.793 8.927
> Ymin, Ymax, Ymax-Ymin: 45.236 58.330 13.094
> Zmin, Zmax, Zmax-Zmin: 22.565 36.388 13.823
> beginning box center at level 1 26.500 52.000 29.500
> beginning box center at level 2 26.500 52.000 29.500
> Grid dimension at level 1 5 9 9
> Grid origin corrected at level 1 14.500 32.000 9.500
> Grid dimension at level 2 33 41 43
> Grid origin corrected at level 2 18.000 41.500 18.500
> PB Bomb in setgrd(): focusing grid too large 2
> reset fillratio to a larger number 2.000
>
>
>
>
> ________________________________
> From: Ray Luo <ray.luo_at_uci.edu>
> To: AMBER Mailing List <amber_at_ambermd.org>
> Sent: Monday, 18 May, 2009 11:13:30 PM
> Subject: RE: [AMBER] Error running MM _PBSA.pl script
>
> Vikas,
>
> Can you take a lot of your pbsa_lig.8.out? There should be an error
> message
> inside before the premature termination of the program.
>
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900 Email: rluo_at_uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf
> Of Vikas Sharma
> Sent: Monday, May 18, 2009 5:00 AM
> To: amber
> Subject: [AMBER] Error running MM _PBSA.pl script
>
> Dear All,
>
> I am using AMBER10... I am using MM PBSA for calculating Binding free
> energy
> of a ligand...
>
> i ran 1 ns production MD..
>
> i used the following commands:
>
> mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log and
>
> mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>
>
>
> After i run mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log i
> get
> the following error
>
>
>
> /opt/amber10/exe/sander -O
> -i pbs a_lig.in -o pbsa_lig.8.out -c
> /home/bharatam/amberresults1/vikamb_q1results/snap shot_lig.crd.8 -p
> /home/bharatam/amberresults1/vikamb_q1/mol.prmtop not successful
>
>
>
> mol is the name of my ligand...
>
>
>
> How can i overcome this error?????
>
> Please help...
>
>
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