It seems like you don't have ZN data in your atmtypenumbers file.
Please check it out.
Wish it could help.
Jack
On Fri, 10 Dec 2004 15:13:37 +0800, Yong Xu <yxu.mail.sioc.ac.cn> wrote:
> 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 - 14:53:00 PST
