AMBER Archive (2004)

Subject: Re: AMBER: No radius found for 2412 Zn Zn

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Fri Dec 10 2004 - 02:21:45 CST

Yong Xu 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.

The error above is unrelated to calculations with delphi, but has to do
with the generation of the pqr file for molsurf calculations. You can
add an appropriate parameter in the function generate_pqr in the file
mm_pbsa_calceneent.pm in $AMBERHOME/src/mm_pbsa to get around.

Best regards

Holger

>
> 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£º
> !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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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
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