AMBER Archive (2008)

Subject: 回复： AMBER: RE: 回复： AMBER: RE: 回复： AMBER: RE: 回复： RE: AMBER: Disturb you for help !?=

From: 捞毛 渔 (yulaomao1983_at_yahoo.com.cn)
Date: Wed Jan 16 2008 - 08:55:37 CST

Dear Dr Yong,
   
  Thanks for you quick reply!
  The prblems as follows:
  But you still have not answered my question, how did you know there is a bond information in your topology file?
  Before docking, there is a bond in the ligand. However, after docking is carried out, I found the some bonds in the ligand is lacking. So I linked them manually. But when I carried out md using amber, I found the bonds disconnected again.
   
  Another problem, when I docked some short peptides into some receptors, I found these ligands could not be treated as a peptide again. (When I extrated these ligands and display them the vmd or sybyl. In the substructure blank, the residues can not be showed. It just consider the ligand as a hetero-molecular) So it could not be loaded into the amber to generate the prmtop and inpcrd files directly. It is really a hard work to solve this problem.
   
  Can you tell me some good way to solve this problem?
   
  Thanks in advance!
   
  Rilei Yu
   

       
---------------------------------
雅虎邮箱传递新年祝福，个性贺卡送亲朋！
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu