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 - 23:53:18 CST

Dear Jack Lei

I think there are Zn data in default atmtypenumbers file. am I right?

line 121 radius 18 1.74 1.97 # Ca calcium
line 122 radius 19 1.25 1.40 # Zn zinc (traditional radius)
line 123 radius 20 1.17 1.40 # Cu copper (traditional radius)
line 360 # Heroes of SOD
line 361 * CU 20
line 362 * ZN 19

should I change ZN to Zn?
is amber program case-sensitive?

======= 2004-12-10 09:49:00 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======

>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_at_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£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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>> The AMBER Mail Reflector
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>
>
>smg

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

Best regards!
                                 
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Yong Xu
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡yxu_at_mail.sioc.ac.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-12-11
===========================================================
* 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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