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
.
.
.       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 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
 ) )
.
.

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 tell me how to get around this problem.

Thanks a bunch

- Vijay Reddy

e-mail: reddyv at scripps.edu