AMBER Archive (2008)

Subject: Re: AMBER: LEap error message for parmBSC0 force field

From: Cenk Andac (
Date: Thu Apr 03 2008 - 07:52:37 CDT

Hi Tom,

Thank you for responding.

here is how I loaded the force field libraries and parameters in LEap.

>source leaprc.rna.ff99
Sourcing: /usr/local/amber9/dat/leap/cmd/leaprc.rna.ff99
Log file: ./leap.log
Loading parameters: /usr/local/amber9/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading library: /usr/local/amber9/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber9/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber9/dat/leap/lib/solvents.lib
> parmbsc0=loadamberparams parmbsc0.params
Loading parameters: ./parmbsc0.params
Reading force field modification type file (frcmod)
Reading title:
torsion chi y gamma
> loadoff all_nucleic.parmbsc0.lib
Loading library: ./all_nucleic.parmbsc0.lib

the improper torsion error messages pop-up with ' verbosity 2 ' only. However,
there appears that the missing improper torsions are already added eventually by LEap.
 ** Warning: No sp2 improper torsion term for OS-H1-CI-CT
        atoms are: O5' H5'2 C5' C4'
 ** Warning: No sp2 improper torsion term for H1-H1-CI-CT
        atoms are: H5'1 H5'2 C5' C4'
  1 C1'<RA5> - C8<RA5> - N9<RA5> - C4<RA5>
  1 C1'<RU3> - C6<RU3> - N1<RU3> - C2<RU3>
  1 C4<RU3> - H3<RU3> - N3<RU3> - C2<RU3>
  1 C5<RA5> - N6<RA5> - C6<RA5> - N1<RA5>
  1 C5<RU3> - O4<RU3> - C4<RU3> - N3<RU3>
  1 C6<RA5> - H61<RA5> - N6<RA5> - H62<RA5>
  1 C6<RU3> - H5<RU3> - C5<RU3> - C4<RU3>
  1 N1<RA5> - H2<RA5> - C2<RA5> - N3<RA5>
  1 N1<RU3> - H6<RU3> - C6<RU3> - C5<RU3>
  1 N1<RU3> - N3<RU3> - C2<RU3> - O2<RU3>
  1 N9<RA5> - H8<RA5> - C8<RA5> - N7<RA5>
 total 11 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)

Thomas Cheatham III <> wrote:
> I keep getting the following error message
> when I try to save a topology file for a 2nt RNA molecule
> using the new parmBSC0 force field. Could someone please
> clarify if I am missing something with the installation of the
> parmBSC0 force field?
> >verbosity 2
> > x=sequence {RA5 RG3}
> Sequence: RA5
> Sequence: RG3
> Joining RA5 - RG3
> > edit x
> > saveamberparm x a.prmtop a.x

...without seeing what you are loading (in terms of the leaprc and what
residue/topology, library, or parameter files) it is tricky to determine,
but my guess is that you didn't load-up all the necessary library/force
field files as it is complaining about impropers...

I would try:

tleap -f $AMBERHOME/dat/leap/cmd/leaprc.rna.ff99
bsc0 = loadamberparams frcmod.parmbsc0

followed by the rest of your script.

-- tec3



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