AMBER Archive (2009)

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

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Tue May 19 2009 - 13:21:47 CDT

Dear Hui Liu

Thanks a lot for the reply...
Thanks for the attachment..
I have made the change you suggested in the file mm_pbsa_createinput.pm.
I have attached the same file(after making the change) below...

I have another question that in my file i dont have the line: print OUT " pbtemp = 300.0,\n";

will this create any trouble...

.

# Here, only REFE
== 0 calculations are allowed, whereby the reference state
    # is assumed to be INDI/INDI.
    # Hence, only one pbsa calc with EXDI/INDI is performed,
    # and the result taken is the reaction field energy
    # (given as "ELE" in the pbsa output).
    # Consider scaling of coulombic interactions as well (by DIELC) if using
INDI != 1.
    # If ISTRNG > 0.0, only one
calculation is done here (compared to delphi).
    # For NLPB, see work of Tsui & Case, J. Phys. Chem. B 2001, 105,
11314
    # and salt_contrib and process_phi scripts in delphi directory.
    # Here, a PBTEMP of 300K is used to
compute the Boltzmann factor for the salt effect.
    # If a different temperature is specified here, also correct the factor
for
    # kcal/mol -> kT conversion in the subroutine calc_pbsa.
    print OUT "
&pb\n";
    print OUT " epsin = ${epsin}, epsout = ${epsout},\n";
    print OUT " istrng = ${istrng}, radiopt = ${radiopt},\n";
    print OUT " sprob = ${sprob}, space = ${space},\n";
    print OUT " maxitn = ${maxitn}, npopt = ${npopt}, dbfopt = 1,\n";
    print OUT " cavity_surften = ${cavity_surften}, cavity_offset = ${cavity_offset},\n";
   print OUT " fillratio = 4.0 " ;
    print OUT " npbverb= 1\n";
    print OUT " &end\n";

________________________________
From: liuhui <fredliu1_at_sohu.com>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Tuesday, 19 May, 2009 9:45:24 PM
Subject: Re: [AMBER] Error running MM _PBSA.pl script

Dear Vikas Sharma,
  The fillratio parameter should be added to the input file for pbsa
(pbsa.in), not that for mm_pbsa.pl(binding_energy.mmpbsa).
  Alternatively, you can just copy the attachment file to
$AMBERHOME/src/mm_pbsa/, and replace your original mm_pbsa_createinput.pm
file (I only added "fillratio=4.0" there, and without any other
modification).

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 11:02 PM
To: "amber" <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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