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
---------------------------------
ÑÅ»¢ÓÊÏä´«µÝÐÂÄê×£¸££¬¸öÐԺؿ¨ËÍÇ×Åó£¡
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jan 20 2008 - 06:07:06 PST
