AMBER Archive (2008)

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

From: Yong Duan (duan_at_ucdavis.edu)
Date: Tue Jan 15 2008 - 22:16:10 CST

Mr. Yu:
 
There is no bond information in PDB. Therefore, to show bonds the program
will have to either use the template or use distance.
 
But you still have not answered my question, how did you know there is a
bond information in your topology file? This is the most crucial
information.
 
 
yong
 
-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
捞毛 渔
Sent: Tuesday, January 15, 2008 5:25 PM
To: amber_at_scripps.edu
Subject: 回复： AMBER: RE: 回复： AMBER: RE: 回复： RE: AMBER: Disturb you
for help !?=

Dear Dr Yong,

You received "core dump" error message?
Yes, just this message, then the program stopped.
 Miminized by sander?
Yes, I use sander to minimize, First I restrained the whole molecular, while
only the TIP3BOX was minimized. This step1 these was no error. But when the
restraint was removed, in the step2 the error appeared.
 Then, how did you realize the bonds are broken?
I just use ambpdb to transfer the out put file of step1 to the pdb form, and
visual them in the sybyl.
 
I have attached these files to this email.
 
Thanks for your help in advance!
 
Best wishes
 
Rilei Yu

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