Hi Modellers,
I understand that it's not a good idea using Modeller to model the very
small peptdie(Here I tried to model the pentapeptide). And I've read the
reply posted by Fiser about forcing modeling to deal only with sidechains
and retain the same backbone conformation. However, I'd like to know if
it's possible to achive the same goal by setting the "SET DEVIATION =
0.0'.
I have built different models by different .top files. The first one is
with 'SET DEVIATION= 0.0'. And the second one, in addition to 'SET
DEVIATION= 5.0', is included a subroutine called 'select_atoms'. Then the
rms among models and templates are around 0.435-1.774. Can you please help
me explain the results? I don't know how much meanings my models have.
Thanks very much.
Best regards,
Violet
Violet(Chiung-wen) Chang, Ph.D. Student
Department of Physiology and Biophysics and Institute for
Computational Biomedicine, Mount Sinai School of Medicine
One Gustave L. Levy Place, Box 1022, New York, NY 10029
phone: (212) 241 1611