AMBER Archive (2009)

Subject: [AMBER] DG improper torsion problem, two missing parameters

From: Youn Kyeung Lee (
Date: Fri Oct 09 2009 - 02:02:03 CDT

I'm running amber to study DNA stability, and I got some problem.

I checked 'DG.prep' file(from xleap by typing 'saveamberprep DG DG.prep'),
and I could see there are 8 improper torsions assigned for Guanine.
 C4 C8 N9 C1'
 H8 N9 C8 N7
 C6 C4 C5 N7
 C5 N1 C6 O6
 C6 C2 N1 H1
 N2 N1 C2 N3
 C2 H21 N2 H22
 C5 N9 C4 N3

However when I tried to get prmtop file,
I got warning messages as below
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4

So I could only have 6 improper torsion applied.
Did I do something wrong?
If not, why does amber prep file assign 8 improper torsions for Guanine
without the corresponding parameters for them?
Should I make another frcmod file for these missed improper torsion?
Is there any library file or frcmod file that I have to load?

here's my tleap input file.
source leaprc.ff03
loadamberparams frcmod.parmbsc0
(this problem is irrelevant to parmbsc0, I tried not to load this frcmod,
but there still exist the problem)

DNA=DNA.pdb (this is just normal DNA)
addions DNA Na+ 0
saveamberparm DNA DNA.prmtop DNA.inpcrd
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