Subject: CCL: DOCK: prepare a mol2 file for receptor

From: Jinsong Zhao <zh_jinsong/at/yahoo.com.cn>
Date: Tue, 7 Dec 2004 00:52:28 +0800 (CST)

Dear all,

Preparation of a mol2 file for receptor seems a crucial step in
DOCKing. I find it's very difficult even I can use SYBYL.

Firstly, I am not sure that histidine residues should be named to HIS,
HIP, HID or HIE. And cysteine residues is also the problem. Are there
any conventions?

Secondly, how to avoid the non-integer charges for certain residue?
Does it mean that if a residue contain missing atom, then it will
charge a non-integer charges?

Any suggestions will be really appreciated! Thanks in advance!

Best wishes,
Jinsong

=====
(Mr.) Jinsong Zhao
Ph.D. Candidate
School of the Environment
Nanjing University
No.22 Hankou Road, Najing 210093
P.R. China
E-mail: zh_jinsong/at/yahoo.com.cn

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