AMBER Archive (2009)

Subject: [AMBER] thymidine monophosphate parametrization

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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

• application/octet-stream attachment: TMP.prepin

• application/octet-stream attachment: TMP.frcmod

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