AMBER Archive (2009)

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

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Thu Jun 18 2009 - 07:49:31 CDT

Thank you Bill! I have carried out some simulations and CG atoms in
carbohydrates behave fine so I think these warnings do not lead to
problems.
In ff03 there is C* atom type which is related to a sp2-hybridized
carbon within 5 memb. ring of TRP.

Best regards,

Sergey

Bill Ross wrote:
>> Could you, please, check the list of files I'm downloading in leap
>>
>
> I haven't used amber for years (I worked on leap for over 5 years
> once), so am too out of date to comment on the files. Questions
> that come to mind are: are the relevant atoms in protein or
> glycam residues? Are atom types consistent across the two ff's?
>
> Bill
>
> >>> ** 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 =20
> >> case, I do not understand why a sp2 atom is found among the =20
> >> 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 ?
> >>
> >
> > I believe what leap is calling sp2 may be any atom with 3 atoms
> > bonded to it. Does this apply here?
> >
> > Bill
> >
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>
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