(Fwd) Torsion Angle Dynamics for Nucleic Acids

[Vijay Reddy]

Hello all,

I am trying to setup torsion angle dynamics for nucleic acid (RNA) associated
with a protein.

for the following "torsion-topology" statement:

dyna tors
   topology

{* All dihedrals w/ (force constant > 23) will be locked *}
      {* This keeps planar groups planar *}
      kdihmax = 23.
:
:
:
       evaluate ( $nucl = 1 )
       while ( $nucl le 10 ) loop cut
       free bond ( resid $nucl and name C3' ) ( resid $nucl and name C4' )
          evaluate ( $nucl = $nucl + 1 )
       end loop cut
:
:
:

! fix group ( resn CYT and ( select the non-hydrogen atoms in the base ) )

!      fix group ( resn CYT and not ( name O5' or name C5' or
!      name C4' or name O4' or name C1' or name C2' or name O2' or
!      name C3' or name O3' or name P or name O1P or name O2P ))

 fix group ( resn CYT and not (
 name N1 or
 name C6 or
 name C2 or
 name O2 or
 name N3 or
 name C4 or
 name N4 or
 name H41 or
 name H42 or
 name C5
 ) )

:
:
end
end

I end up getting the error:

 -------------------------- Torsion Topology ----------------------------------
   WARNING: A single-group tree does not have an
            acceptable base.
            Please alter topology and re-run.
            This is usually due to isolated atoms.
            Delete them or fix them to proceed.

 %TORSION:TOPOLOGY-ERR: Fatal Topology Error
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 BOMLEV=    0 reached.  Program execution will be terminated.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 Subroutine DIE called . Terminating


Can someone please tell me, how to get around this problem.

Thanks a bunch

- Vijay Reddy
e-mail : reddyv at scripps.edu



---End of forwarded mail from "Vijay Reddy" <reddyv at noda.scripps.edu>