We are trying to join a dsRNA with a peptide using HyperChem. The moment we are trying to invoke the model builder, the double stranded structure just mashes up in a weird mesh like thing. Whenever we are trying to optimize the geometry using steepest descent or conjugate gradient or Newton-Raphson, a lot of Oxygen appears from nowhere (which do not show up in other visualization tools like PyMol or VMD). And when we are trying to join the peptide without doing the geometry optimization (the most unscientific thing I have ever heard of), the connecting bond just becomes a long stretch of line (which it should not be, because there's a permissible limit of bond length, isn't it???)
Can anybody shed any light on how to do this job in HyperChem??? We are open to other softwares also, if required.
Try using academic version of maestro:
https://www.schrodinger.com/maestro
take a look at this video
https://www.youtube.com/watch?v=J2QSnP9qLIs
best,
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