Dear all,
I was checking some interactions in a pairwise calculation (MMPBSA
perl, AMBER11) and I've notice some unrealistic or at least high
values in the electrostatic term.
For instance the electrostatic interaction between residue 13 (GLU)
and 123 (LYS) is -5.330 kcal/mol altough they are 32 angstroms far
away. This seems related to the cut parameter. If instead of the
default value of 999.0 (in perl PBSA) one uses 9.0 then the pairwise
interaction falls to 0 which seems more reasonable.
TDC 13-> 123 0.000 -0.000 -5.330 5.263 0.000
Therefore, my question is why particle-mesh Ewald (PME) procedure
which handles long-range electrostatic interactions calculate such a
value at 32 angstoms of distance? I can understand that with a cutoff
of 999.0 the procedure includes long interactions but at 32 angstroms
.... I would think that there is no electrostatic interaction. What
am I missing? What I am doing wrong?
All comments welcome. All the best.
Campa,
All necessary files to reproduce this results can be provided.
------------------------------------------------------------------
File generated by mm_pbsa.pl. Using MM GB MS
&cntrl
ntf = 1, ntb = 0, dielc = 1.0,
idecomp= 4,
igb = 2, saltcon= 0.00,
offset = 0.09,
intdiel= 1.0, extdiel= 80.0,
gbsa = 2, surften= 1.0,
cut = 999.0, nsnb = 99999,
imin = 1, maxcyc = 1, ncyc = 0,
&end
Residues considered as REC
RRES 1 208
END
Residues to print
RES 1 208
END
END
---------------------------------------
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Received on Tue Mar 19 2013 - 08:30:03 PDT
