VMD-L Mailing List

From: parinaz bashirbanaem (parinaz.bashirbanaem_at_gmail.com)
Date: Sun Jan 28 2018 - 04:16:44 CST

Hi everyone,

I'm working with DNA and trying to make PDB file from crystal structure by
VMD. But unfortunately, when are added hydrogens by VMD, in the case of
amine functional group geometrical structure converts to flat instead of
trigonal pyramidal. Could you lead me towards how to correct this task?

Thank you very much for any suggestion.

Best regards,

Parinaz.