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AMBER Archive (2009)Subject: [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom
From: suhaib sh (suhaib.shekfeh_at_gmail.com)
Hello everybody
I am trying to run mm_pbsa calculation on the snapshots that I got from MD
Unfortunately two of my ligands has halogen atoms Flourine and Bromine ...
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
unfortunately that didnt work with me
last parameters I used were :
#
#
could anybody give me some advices .. by the way the results on other
in some articles like : molecular dynamics simulation and free energy
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
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-Universitt Halle-Wittenberg _______________________________________________ AMBER mailing list AMBER_at_ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
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