On Mon, Dec 08, 2014, ROOPALI VERMA wrote:
>
> I am trying to create my prmtop and inpcrd file from tleap of amber12 for
> that i have created leaprc file
>
> source leaprc.ff96
My geuss is that the error is in the "source leaprc.ff96" step: this is not a
recommended ff, and its leaprc file is in the "oldff" directory. Hence, no
protein libraries were loaded. You should see the following line in your
output:
Could not open file leaprc.ff96: not found
[Developers: I'm thinking we should make this a fatal error, rather than just
a warning.]
You should be *sure* that this is the forcefield you really want. It has
rather poor secondary structure preferences. I am aware of claims that
this can be somewhat ameliorated by combining it with certain GB models, but
am not (personally) fully convinced. You should also consider using ff14SB
plus igb=8:
%A H. Nguyen
%A J. Maier
%A H. Huang
%A V. Perrone
%A C. Simmerling
%T Folding Simulations for Proteins with Diverse Topologies Are Accessible in
Days with a Physics-Based Force Field and Implicit Solvent
%J J. Am. Chem. Soc.
%V 136
%P 13959-13962
%D 2014
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 08 2014 - 05:00:02 PST
