AMBER Archive (2007)

Subject: To Mr. Ross Walker Re: RE: AMBER: How to add semi-experience parameter in divcon?

From: clarkzhy (clarkzhy_at_mail.bnu.edu.cn)
Date: Thu Jun 21 2007 - 20:19:23 CDT

Mr. Ross Walker,
   Sure, I have a reference for Calcium paramerer. It is: J. J. P. Stewart, Optimization of parameters for semiempirical methods IV: extension of MNDO, AM1, and PM3 to more main group elements, J Mol Model (2004) 10:155–164.

   But, These parameters in this paper are different with that in Spartan. I am puzzled on it.
 atnum 20
n 4.0
uss -11.35010387
upp -10.34987587
betas -10.45737746
betap 5.10954286
zs .69567815
zp 1.05125946
alpha 1.90107319
eisol -16.94020844
gss 5.76
gsp 5.04
gpp 4.32
gp2 4.00
hsp .52
a1 .52766269
b1 10.0
c1 .51696708
a2 -.00139269
b2 6.0
c2 2.56686118
hform 42.6
zval 2.0000000

This is the Calcium parameters from Spartan.


Would you please tell me why they are different, and how to add parameters to divcon?




clarkzhy
2007-06-22



发件人： Ross Walker
发送时间： 2007-06-19 23:50:05
收件人： amber_at_scripps.edu
抄送：
主题： RE: AMBER: How to add semi-experience parameter in divcon?

Dear Clarkzhy,

Which semiempirical method do you have Calcium parameters for? Do you have references for these parameters? I assume this is a true atom and not a "sparkle". If you have the complete set of parameters I can help you add them to either Amber 9's implicit QM/MM or Divcon.

All the best
Ross

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of clarkzhy
Sent: Tuesday, June 19, 2007 07:23
To: amber_at_scripps.edu
Subject: AMBER: How to add semi-experience parameter in divcon?


Hello, everyone!

Recently, I need to use QM/MM method in Amber9 to deal with some protein system with metal. But, there are some missing parameters in the program, such as Ca2+ ions. Does angone could help me? Mr. David A. Case, would you please tell me how to add the papameter to the program-divcon?



clarkzhy
2007-06-19

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