AMBER Archive (2009)

Subject: 回复： [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom

From: 廖青华 (fantastic_0919_at_yahoo.com.cn)
Date: Thu Jul 02 2009 - 23:53:09 CDT

Hi sir,
 In order to have MM-PBSA working with ligands having halogen atoms, it is necessary to include halogen radii in mm_pbsa_calceneent.pm
(assuming one is using MOLSURF and not LCPO). you must insert F, Cl and Br radii in this file:
                  "N" => 1.550 + 1.400,
                  "H" => 1.200 + 1.400,
                  "C" => 1.700 + 1.400,
                  "O" => 1.500 + 1.400,
                  "P" => 1.800 + 1.400,
                  "S" => 1.800 + 1.400,
                  "FE" => 1.300 + 1.400,
                  "Na+" => 1.200 + 1.400,
                  "Cl-" => 1.700 + 1.400,
                  "MG" => 1.180 + 1.400,
                  "F" => 1.470 + 1.400,
                  "Cl" => 1.750 + 1.400,
                  "Br" => 1.850 + 1.400,
                  "I" => 1.980 + 1.400, 

See J Phys Chem 1964, 68, 441 or other paper. You can find such papers. http://www.casper.organ.su.se/reference/bondi.pdf.
 
This is what my teacher  told me to do, and it worked.
 
Best wishes!
 
Qinghua Liao

 fantastic_0919_at_yahoo.com.cn or fantasticqhl_at_yahoo.com

________________________________
发件人： suhaib sh <suhaib.shekfeh_at_gmail.com>
收件人： amber_at_ambermd.org
已发送： 2009/7/2(周四), 下午9:18:05
主题： [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom

Hello everybody

I am trying to run mm_pbsa calculation on the snapshots that I got from MD
simulations using AMBER9 with optimized Radii by by Tan and Luo

Unfortunately two of my ligands has halogen atoms Flourine and Bromine ...
so for these two inhibitors the run finished directly giving in
pbsa_com.1.out

PB Bomb in pb_aaradi(): No radius assigned for atom        2706 Br1 br

PB Bomb in pb_aaradi(): No radius assigned for atom        2705 F1  f

I have searched already the archive and find advices from Luo and Case that
swtiching off GBSA calculation could let the calculations proceed

unfortunately that didnt work with me

last parameters I used were :

#
PREFIX                snapshot
PATH                  ../snapshots
#
COMPLEX              1
RECEPTOR              1
LIGAND                1
#
COMPT                ../z.prmtop
RECPT                ../x.prmtop
LIGPT                ../y.prmtop
#
GC                    0
AS                    0
DC                    0
#
MM                    1
GB                    1
PB                    1
MS                    1
#
NM                    0
#

#
PROC                  2
REFE                  0
INDI                  1.0
EXDI                  80.075
SCALE                1.5
LINIT                1000
PRBRAD                1.4
ISTRNG                0.0
RADIOPT              1
NPOPT                1
CAVITY_SURFTEN        0.0072
CAVITY_OFFSET        0.00
#
SURFTEN              0.0072
SURFOFF              0.00
#

could anybody give me some advices .. by the way the results on other
ligands was much more better than the default radii setting .. that is why I
wanna continue with this method...

in some articles like : molecular dynamics simulation and free energy
calculations of symmetric flouro-substituted diol-based HIV-1 protease
inhibitors

by Chen et. al. Journal of molecular structure: Theochem 899 (2009)

they use a radii for Flourine as 1.4 .. I found in the interenet advices as
assigning 1.4 for flourine and 1.7 for Br.

but how could I put this parameters in Sander for PBSA calculations

thanks in advance 

-- 
Pharmacist. Suhaib Shekfeh
Medicinal Chemistry
Institute of Pharmacy
Martin-Luther-Universit鋞 Halle-Wittenberg
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