dear Amber !
I have build a model for DNA junction.
I have a problem in running the minimization in vaccum, when I load the molecule in leap it have not
showed any error .
1. I loaded the molecule and when i saved the parameter file it gave the following warning
--------------------------------------------------------------
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-C-CB-CB
atoms are: N7 C6 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 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 N*-CB-CB-NC
atoms are: N9 C5 C4 N3
------------------------------------------------------
but the .inpcrd and .prmtop files got saved
2) when i do the minimization in vaccum it
sander got stoped and it gave the following error
----------------------------------------------------------
At line 1262 of file _ew_box.f
Fortran runtime error: Bad value during integer read
----------------------------------------------------------
what is the problem with the molecule and what one should do to
correct it
thanks in advance
balaji
UOM
_________________________________________________________________
Stay updated! Add Facebook, LinkedIn, MySpace & Hi5 friends to your Windows Live network instantly. Add Now!
http://profile.live.com/webactivities/?mkt=en-in_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 02 2009 - 05:00:02 PDT
