AMBER: about radius of Br in MMPBSA calculation

From: Yong Xu <>
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/ 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 - 03:53:00 PDT
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