AMBER Archive (2009)

Subject: [AMBER] MM_PBSA Problem (no radius for ion)

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Thu Dec 17 2009 - 13:39:49 CST

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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