AMBER Archive (2004)

Subject: AMBER: No radius found for 2412 Zn Zn

From: Yong Xu (yxu_at_mail.sioc.ac.cn)
Date: Fri Dec 10 2004 - 01:13:37 CST


Dear Amber-users

I performed MM-PBSA simulation and encounter some problem.
when I do mm_pbsa.pl mm_pbsa.in >mm_pbsa.log
system give this info:
No radius found for 2412 Zn Zn

Then I modify "my_delphi.crg" and "my_delphi.siz" by adding Zn parameter, but this information still remain.

which file should I modify and what should I add?

Any suggestion would be very appreciated!

=================
more my_delphi.crg
 
!Amber parm94 charges
atom_resnumbc_charge
N MET 1 0.1592
:
:
:
NA+ CIP 1.0000
CL- CIM -1.000
Zn Zn 2.000
C0 C0 2.000
(I added the last two lines

================
my_delphi.siz
!my siz based on PARSE
:
:
:
:
Mg 0.99
Zn 1.10
C0 1.71

(beside Zn2+, there are also Ca2+ ions, so I also added C0 for Ca2+ ions)

        

Best regard!

        Yong Xu
        yxu_at_mail.sioc.ac.cn
          2004-12-10

===========================================================
* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Science
           
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
        
* Email: yxu_at_mail.sioc.ac.cn
* yxuemail_at_sina.com
===========================================================

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