[gmx-users] Energy Minimization nan && WARNING 1 [file "blah.itp", line 1020]: No default G96Angle types, using zeroes

Joern Lenz JLenz at zbh.uni-hamburg.de
Wed Aug 16 16:32:48 CEST 2006

dear gromacs users,
i am new to gromacs (using version 3.3.1) and trying to simulate an enzyme 
which is covalently bound to a piece of dna i.e. a tyrosine is connected to 
the dna backbone establishing a phosphodiester group.
but each time i try to start the simulation using the G43a1 forcefield there 
occurs a warning like 
WARNING 1 [file "blah.itp", line 1020]:
No default G96Angle types, using zeroes 
WARNING 39 [file "blah.itp", line 1509]:
No default Proper Dih. types, using zeroes

i browsed to the mailing list archive and found lots of problems similar to 
mine but - forgive me -  i am not able to fix my problem with these hints.
i know that i have to add these angles and dihedrals in the itp or rtp files. 
But where exactly and how.

one example oif a missing angle is the connection from one nucleeotide to the 
next in the DNA (O3* - P - O1P).
Can anyone tell me how to add the missing lines and where to do that exactly 
(perhaps with a little example) ???
That would be of great help for me. Otherwise I will die unhappy ...

Another problem is: where to tell GROMACS that there is a connective bond, 
angle, dihedral between an aminoacid (the phenolic group of tyrosine) and the 
DNA backbone ? 

So if you have any suggestions that could help me, be so kind and try to 
answer my question.
Have a nice day

More information about the gromacs.org_gmx-users mailing list