AMBER Archive (2009)

Subject: [AMBER] GLYCAM: warnings by writing topology

From: Sergey Samsonov (
Date: Wed Jun 17 2009 - 01:38:56 CDT


I'd like to carry out MD simulations with the systems consisting both of
proteins and carbohydrates. So I'm trying to use GLYCAM06 in AMBER10.
 From what I've learnt from the previous posts to the Mailing List, I
use both ff03 and GLYCAM06 leaprc files as follows in t/xleap:

source leaprc.ff03
source leaprc.GLYCAN_06

It seems like all the needed files are loaded and I can proceed. When I
create the topology and coordinates files with the systems containing
saccharides it also looks that they are created properly. However, I
have the following warnings in the log.file:

** Warning: No sp2 improper torsion term for CG-H1-CG-OH
      atoms are: C3 H2 C2 O2
** Warning: No sp2 improper torsion term for CG-H1-CG-CG
      atoms are: C3 H2 C2 C1
** Warning: No sp2 improper torsion term for CG-OH-CG-CG
      atoms are: C3 O2 C2 C1
... and so on

What wrong I could do to get this or should I ignore these warnings?

Thank you very much in advance and best regards,


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