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