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

From: suhaib sh <suhaib.shekfeh.gmail.com>
Date: Thu, 2 Jul 2009 14:18:05 +0100

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-Universitšt Halle-Wittenberg
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 06 2009 - 12:35:49 PDT
Custom Search