AMBER Archive (2002)

Subject: xleap problem

From: FyD (fyd_at_u-picardie.fr)
Date: Thu Jun 27 2002 - 03:20:53 CDT

Dear All,

I used "xleap" to generate "prmtop" and "prmcrd" files of an unusual
unit. I checked the generated improper FF parameters with "rdparm". It
looks like that an improper center has been selected for a CT atom type
by xleap.
See the output of rdparm just below:
....
B 33: 1.000 3.14 2.0 :1_at_H1 :1_at_N1 :1_at_C6 :1_at_C2
(2,1,11,3)
....
Moreover, this oop is totally wrong topologically even if CT would be a
C atom type. Indeed atom numbers 2, 1, 11 and 3 cannot make an improper
dihedral....

I set up the CT atom type for C6 in the OFF library. See below:
....
!entry.MOL.unit.atoms table str name str type int typex int resx
int flags int seq int elmnt dbl chg
...
 "C6" "CT" 0 1 131073 11 6 0.020900
...

After reading http://www.amber.ucsf.edu/amber/Questions/improp.html,
each sp2 atom should be an improper center; not a CT/sp3 atom type....

What could be the problem ?

Thanks, Regards, Francois