Dear AMBER
Today, I have encountered another problem during performing MM-PBSA for my system. My system contains Zinc ion and Calcium ion.
During binding_energy.mmpbsa step, I got the following error:
No radius found for ZN 2647 in residue ZN 172
I searched the AMBER archieve and I found that we should modify the mm_pbsa_calceneent.pm file.
I did add the raidus for my ions, as following:
if(exists $r_del->{"IVCAP"} && ($r_del->{"IVCAP"} == 1 || $r_del->{"IVCAP"} == 5)){
# Prepare for calc of molecular surface
%exp_rad = (
"N" => 1.550,
"H" => 1.200,
"C" => 1.700,
"O" => 1.500,
"P" => 1.800,
"S" => 1.800,
"FE" => 1.300,
"Na+" => 1.200,
"Cl-" => 1.700,
"MG" => 1.180,
"ZN" => 0.740,
"CA" => 0.990,
);
Unfortunately, I still have the same error.
Could any body tell me what should I do? and also are these Radii values for Zinc (0.74) and Calcium (0.99) right?
Thanks in advance
S. Bill
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Received on Thu Dec 17 2009 - 12:00:02 PST
