Re: RE: AMBER: about radius of Br in MMPBSA calculation

From: Yong Xu <yxu.mail.sioc.ac.cn>
Date: Fri, 16 Sep 2005 16:41:30 +0800

Dear Shan Jufang

I am using amber7, I can't find mm_pbsa_calcenent.pm file .
I think in my amber7 install dir, */*/src/mm_pbsa/mm_pbsa_statistics.pm* file may equal to your mm_pbsa_calcenent.pm. but where should I add put the radius value.
I am not familar with programming.

would you like to give me a more detailed guide for this problem!

thanks

Yong
        

======= 2005-09-15 18:00:00 Shan Jufang wrote=======

>Hi, Yong,
>
>Have you added radius for Br in file
>$AMBERHOME/src/mm_pbsa/mm_pbsa_calceneent.pm?
>
>Best,
>Jufang
>
>----Original Message Follows----
>From: "Yong Xu" <yxu.mail.sioc.ac.cn>
>Reply-To: amber.scripps.edu
>To: "amber.scripps.edu" <amber.scripps.edu>
>Subject: AMBER: about radius of Br in MMPBSA calculation
>Date: Thu, 15 Sep 2005 10:36:35 +0800
>
>Dear, all
>
>how to set radius of Br in MMPBSA calculation. there is a Br atom in the
>ligand.
>what should be added in atmtypenumbers and my_parse_delphi.siz file?
>
>I have append one line "Br 1.50" at the end of my_parse_delphi.siz.
>
>but MMPBSA calculation still failed and give following info:
>
>=>> Creating input
> Sander input
> Delphi input
>
>=>> Calculating energy / entropy contributions
> Calc contrib for ../1_snap/ptp1b_p15_com.crd.1
> Calc MM/GB/SAS
> Generate PDB
> Calc PB
> Run 0
> Generate PQR
> No radius found for 4592 MOL Br1
>Died at /disk8/yxu/bin/mm_pbsa.pl line 1337, <PDB> chunk 4594.
>
>any reply would be very appreciated!
>
>
>Best regard!
>
>Yong Xu
>yxu.mail.sioc.ac.cn
>2005-09-15
>
>===========================================================
>* 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
>* xuyongch.yahoo.com
>===========================================================
>
>
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= = = = = = = = = = = = = = = = = = = =
                        

Best regards!
                                 
        Yong Xu
        yxu.mail.sioc.ac.cn
          2005-09-16
===========================================================
* 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 Sep 16 2005 - 09:53:03 PDT
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