AMBER Archive (2009)

Subject: Re: [AMBER] GLYCAM: warnings by writing topology

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Jun 17 2009 - 02:30:26 CDT

Dear Sergey,

> 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?

Warnings are not errors: Usually, you can proceed... However in your
case, I do not understand why a sp2 atom is found among the
CG-H1-CG-OH atom types for instance...

more $AMBERHOME/dat/leap/cmd/leaprc.GLYCAM_06
[...]
addAtomTypes{
         { "CG" "C" "sp3" }
         { "H1" "H" "sp3" }
         { "OH" "O" "sp3" }
}

None of these atoms are sp2 but sp3. right ?

regards, Francois

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