AMBER Archive (2008)

Subject: AMBER: RE: 回复: RE: AMBER: A problem to loadup the molecular in the xleap

From: Yong Duan (
Date: Sat Jan 19 2008 - 14:44:25 CST

That was why I asked you how much do you know the basic theory about
molecular modeling.
Briefly, prmtop file describes the molecular connectivity (bonds) and
associated parameters (partial charges, force constants, etc.). Many of
these parameters are linked to "atom types" (e.g., mass, bond parameters
...). If the atom types and the associated parameters are not defined in xx.
frcmod, Leap can not produce prmtop file. Take a look at the .frcmod file to
see if these "bond type and atom types" are in it or not. If they are not,
you have to develop the parameters by your self.
-----Original Message-----
From: [] On Behalf Of
捞毛 渔
Sent: Saturday, January 19, 2008 8:31 AM
Subject: 回复: RE: AMBER: A problem to loadup the molecular in the xleap

Dear Dr Yong,
The errors were just as I had not loaded up the imichange.prepin and
imichange.frcmod. It said that some bond type and atom types could not be
Tonight I ran the program again, but I still could not save the file. May be
loading up the file in the format of mol2 was not the same as loading up the
pdb file? I did all the thing as the tutorial.
Another problem, when I saved the protein file (the receptor) as mol2 in
sybyl. Then i loaded it up in the xleap, and displayed it. Unfortunately,
some bonds of this receptor were also changed! So the receptor could not be
saved in xleap to get the prmtop and inpcrd files also!
I had attached these files to the email. I really hope you can provide me
some help.
Best wishes
Rilei Yu



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