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