Dear Amber users,
Using Amber9, I am currently trying to parametrize thymidine
monophosphate correctly. During a minimization-equilibration in NAMD,
the 2 OH groups of the phosphate group get too close to each other.
According to your experience, what should I add to the attached prepin
(output of antechamber) or frcmod (output of parmchk) files to avoid
this problem?
Thank you in advance.
Best regards,
Yvonne Westermaier
Received on Fri Jul 24 2009 - 10:09:51 PDT
