AMBER Archive (2004)

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

From: Yong Xu (yxu_at_mail.sioc.ac.cn)
Date: Fri Dec 10 2004 - 03:15:14 CST

Dear Gohlke,

I can't find mm_pbsa_calceneent.pm in $AMBERHOME/src/mm_pbsa.
there are only mm_pbsa_statistics.pm
and I can't grep generate_pqr out from all files in that dir.

have I installed it correct?

======= 2004-12-10 09:21:00 您在来信中写道：=======

>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：
>> !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
>> ===========================================================
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>--
>++++++++++++++++++++++++++++++++++++++++++++++++++
>Dr. Holger Gohlke
>
>J.W. Goethe-Universit鋞
>Fachbereich Biologie und Informatik
>Institut f黵 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
>++++++++++++++++++++++++++++++++++++++++++++++++++
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
>
>smg

= = = = = = = = = = = = = = = = = = = =
                        

Best regards!
                                 
　　　　　　　　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
===========================================================
　　　　　　

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu