AMBER Archive (2008)

Subject: AMBER: LEap error message for parmBSC0 force field

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Tue Apr 01 2008 - 18:31:17 CDT

Dear amber community,

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
Checking Unit.
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 ** 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-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for OH-H1-CI-H1
        atoms are: O5' H5'1 C5' H5'2
 ** Warning: No sp2 improper torsion term for OH-H1-CI-CT
        atoms are: O5' H5'1 C5' C4'
 ** Warning: No sp2 improper torsion term for OH-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'
 ** 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
 ** Warning: No sp2 improper torsion term for OS-H1-CI-H1
        atoms are: O5' H5'1 C5' H5'2
 ** Warning: No sp2 improper torsion term for OS-H1-CI-CT
        atoms are: O5' H5'1 C5' C4'
 ** 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'
--Impropers:
  1 C1'<RA5> - C8<RA5> - N9<RA5> - C4<RA5>
  1 C1'<RG3> - C8<RG3> - N9<RG3> - C4<RG3>
  1 C2<RG3> - H21<RG3> - N2<RG3> - H22<RG3>
  1 C5<RA5> - N6<RA5> - C6<RA5> - N1<RA5>
  1 C5<RG3> - O6<RG3> - C6<RG3> - N1<RG3>
  1 C6<RA5> - H61<RA5> - N6<RA5> - H62<RA5>
  1 C6<RG3> - H1<RG3> - N1<RG3> - C2<RG3>
  1 N1<RA5> - H2<RA5> - C2<RA5> - N3<RA5>
  1 N1<RG3> - N2<RG3> - C2<RG3> - N3<RG3>
  1 N9<RA5> - H8<RA5> - C8<RA5> - N7<RA5>
  1 N9<RG3> - H8<RG3> - C8<RG3> - N7<RG3>
 total 11 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)

regards,

jenk

       
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