AMBER Archive (2006)

Subject: AMBER:

From: Qingning Shu (qshu_at_mail.rx.uga.edu)
Date: Tue Aug 29 2006 - 08:01:58 CDT

Hi Amber Users:
I have a guanosine-analogue nucleotide ligand in protein complex. I obtained its prepin file accoding to the standard RNA residue. I set the atom types of C1', N9, C8, H8 as CT, N*, CK and H5 respectively. The dihedral angle C1'-N9-C8-H8 should be 0 degree. But during the MD process, this angle changed. It was not 0 degree anymore. I also tried relaxing the standard residue RG using xleap. This dihedral angle also changed. But since purine ring is conjugated, this angle should maintain at 0 degeee. Is it the problem of atom type? could anyone help me? Thank you in advance.

SHU

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