AMBER Archive (2006)

Subject: AMBER: questions about mm_pbsa

From: Weihua Li (whli.ecust_at_gmail.com)
Date: Wed Apr 26 2006 - 22:09:45 CDT

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 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

------------------------------------------------------

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:
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

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