AMBER Archive (2005)

Subject: AMBER: about radius of Br in MMPBSA calculation

From: Yong Xu (yxu_at_mail.sioc.ac.cn)
Date: Wed Sep 14 2005 - 21:36:35 CDT


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_at_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_at_mail.sioc.ac.cn
* xuyongch_at_yahoo.com
===========================================================

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