AMBER Archive (2009)

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

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Wed May 20 2009 - 03:29:42 CDT

Dear Hui Liu

Thanks a lottt...

I got the results after following your suggestions..
thank you

________________________________
From: liuhui <fredliu1_at_sohu.com>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Wednesday, 20 May, 2009 7:50:26 AM
Subject: Re: [AMBER] Error running MM _PBSA.pl script

Dear Vikas Sharma,

  Once I used a PBTEMP of 298K to compute the PB, however, that was changed
to the default 300K for you, and no trouble will be created.

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: Wednesday, May 20, 2009 2:21 AM
To: "AMBER Mailing List" <amber_at_ambermd.org>
Subject: Re: [AMBER] Error running MM _PBSA.pl script

> 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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>
>
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