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.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.mail.sioc.ac.cn
* yxuemail.sina.com
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Received on Fri Dec 10 2004 - 07:53:00 PST
