AMBER Archive (2007)

Subject: AMBER: Ca(2+) parameter

From: Qiang Zhong (zqiang320_at_webmail.hzau.edu.cn)
Date: Thu Aug 23 2007 - 06:01:24 CDT

Dear Amber users:
          I am doing MD simulation, there are 4 Ca2+ in my protein.
I download Ca2+ parameter from AMBER Parameter Database.
They are CAL.dat, CAL.in. I use loadAmberParams CAL.dat
loadAmberPrep CAL.in to load them when I prepare .parm7 and .crd
files. But I get some error message below:

failed to find default bond length KA-KA, types KA-KA
failed to find default bond length KA-KA, types KA-KA
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-KA-KA-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
failed to find default bond length KA-KA, types KA-KA
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-KA-KA-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved

So I modify the file leaprc.ff03 as below:

        { "KA" "Ka" "sp3" }

But error is still there.

Could somebody tell what wrong with it? Thank you very much!

parameter is below:
CAL.dat
Ca2+ vdw parameters from Concanavalin A study
MASS
KA 40.00 0.00

NONB
  KA 1.7900 0.0140

CAL.in
  0 0 2

------calcium--------------
CAL
CAL INT 0
CHANGE OMIT DU BEG
 0.0
   1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.000
   2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000 0.000
   3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000 0.000
   4 KA KA M 29.683 127.561 -18.450 2.00
 
 
DONE
STOP

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