RE: AMBER: about radius of Br in MMPBSA calculation

From: Shan Jufang <>
Date: Thu, 15 Sep 2005 18:00:56 -0400

Hi, Yong,

Have you added radius for Br in file


----Original Message Follows----
From: "Yong Xu" <>
To: "" <>
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
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/ line 1337, <PDB> chunk 4594.

any reply would be very appreciated!

Best regard!

Yong Xu

* 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:

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Received on Thu Sep 15 2005 - 23:53:00 PDT
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