AMBER Archive (2006)

Subject: Re: AMBER: questions about mm_pbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Wed Apr 26 2006 - 20:03:13 CDT

The reason is that the "cutres=12" or "cutres=18" are not inside the
namelist:

&pb
&end

Pleae add it in the right place in mm_pbsa_createinput.pm.

Weihua Li wrote:

> Dear all,
> I want to calculate the binding free energy between ligand and
> protein. The protein contains non-standard residues and a cofactor
> heme. The version is Amber 8.
> (1) When I use/ pbsa/ (not delphi) to calculate, the program gave
> the error: PB bomb in pb_reslist(): maxnbr too small.
> Following previous suggestions, I added the line below to
> ~AMBERHOME/src/mm_pbsa/mm_pbsa_createinput.pm.
> print out " cutres = 12 \n";
> However, PB bombed again. I increased cutres=18, the PB still
> bombed.
> (2) The pbsa_com.1.out gave the following output:
> .....
> 7509 HEM FE 1.130000 1.500000 1.234539
> 7510 HEM NA -0.503000 1.550000 1.512500
> 7511 HEM C1A 0.501000 1.700000 1.549917
> .....
> What I know is that the forth column is partial charge and the fifth
> is PARSE radii, but what is the last column?
> In addition, what file do the PARSE values define in? Could I define
> the PARSE value by myself, just as used by delphi via a
> my_parse_delphi.siz?
>
> Any comments and suggestions are appreciated.
> The mm_pbsa.in and pbsa.in <http://pbsa.in> are enclosed.
>
>
> Best regards,
> Weihua
>
> ==============================
> Weihua Li
> Lab of Molecular Modeling and Design
> School of Pharmacy
> East China University of Science and Technology
> Mailbox 268
> 130 Mei Long Road
> Shanghai 200237,China
> Tel:+86-21-64251190
> E-mail: whli.ecust_at_gmail.com <mailto:whli.ecust_at_gmail.com%20>
>
> ------------------------------------------------------
>
> mm_pbsa.in:
> @PB
> PREFIX N297S
> PATH ../1_snapshot/
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ../com_now.top
> RECPT ../protein_now.top
> LIGPT ../ligand.top
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 0
> PB 1
> MS 1
> #
> NM 0
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2.0
> LINIT 1000
> PRBRAD 1.4
> #
> RADIOPT 0
> SURFTEN 0.00542
> SURFOFF 0.92
> @MM
> DIELC 1.0
> @MS
> PROBE 0
>
> pbsa.in <http://pbsa.in>:
> File generated by mm_pbsa.pl. Using PB
> &cntrl
> ntf = 1, ntb = 0,
> igb = 10, dielc = 1.0,
> cut = 999.0, nsnb = 99999,
> scnb = 2.0, scee = 1.2,
> imin = 1, maxcyc = 0, ntmin = 2,
> &end
> &pb
> epsin = 1.0, epsout = 80.0,
> istrng = 0, radiopt = 0,
> sprob = 1.4, space = 0.5,
> maxitn = 1000
> npbverb= 1
> &end
> cutres = 18
>
>
> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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