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