[AMBER] mmpbsa-bad atom (metal ions)

From: 原翆 <futing.dicp.ac.cn>
Date: Fri, 3 Jun 2011 08:59:26 +0800

Dear AMBER!
Today I have encountered a problem during performing MM-PBSA for my system. My system contains manganese ion, magnesium ion and Calcium ion. During binding_energy.mmpbsa step, I got the following error:

 ??????? No radius found for MN ??
 ??????? No radius found for KA ??

 I searched the AMBER archieve and I found that we should modify the mm_pbsa_calceneent.pm file. But I don't know what are the Radii values for manganese(MN2+) ion and Calcium ion (KA2+)?

Furthermore, how to modify the Amber10/src/sander/mdread.f and Amber10/src/pbsa/mdread.f ?
eg:

! Cl added by UR 5/11-08: radius = 1.8, parameters from S
            else if (atype == 'Cl' .or. atype(1:1) == 'cl') then
               x(l165-1+i) = 1.80d0 + 1.4d0
               x(l170-1+i) = 0.54581d0
               x(l175-1+i) = -0.19477d0
               x(l180-1+i) = -0.0012873d0
               x(l185-1+i) = 0.00029247d0

But how can I get these values [ x(l165-1+i), x(l170-1+i), x(l175-1+i), x(l180-1+i), x(l185-1+i)] for manganese(MN2+) ion and Calcium ion (KA2+)?

Could any body kindly tell me about these parameters and any necessary information ?

Thank you for your kind consideration of this request.

Sincerely: Ting Fu

      

        原翆
        futing.dicp.ac.cn
          2011-06-03
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Received on Thu Jun 02 2011 - 18:30:02 PDT
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