AMBER Archive (2009)

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

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Wed Jun 17 2009 - 04:09:23 CDT

Hi Karl!

Thank you for the help and the useful suggestion.
The strange thing is that I also looked into leaprc.ff03 file and here
CG atom is sp2-hybridized. In both AMBER8 and AMBER10 (though I think
the files are the same anyway):
 
{ "CG" "C" "sp2" }

I deleted this line in leaprc.ff03, loaded leaprc.ff03 and
leaprc.GLYCAM_06 as source files and in this case I didn't get any
warnings in my log file after creation of sugars topology. It is
surprising because I load initial leaprc.ff03 first and I would expect
that after loading also leaprc.GLYCAM_06, the information could be
overwritten but it does not happen.

Best regards,

Sergey

Karl Kirschner wrote:
> Hi Sergey,
>
>
>> However, CG in leaprc.ff03 is sp2-hybridized. Could it be that when I
>>
>
> You are right, that CG is labled as an sp2-hybridized atom. However, I checked
> frcmod.ff03 does not have any CG atom type (same is true for parm99.dat,
> which is loaded with ff03). So, I am not sure why this is included in
> leaprc.ff03. Maybe someone else can comment who knows better.
>
> When we developed Glycam_06, we designated sp3 carbons as CG to distinguish it
> from the other force fields - meaning that almost all of the Glycam torsion
> angles contain a CG atom type, so when it is loaded with a protein force
> field there is no overwriting of the protein torsion parameters.
>
> As a test, if CG is truely not needed by ff03 or parm99, then try deleting it
> from the leaprc.ff03 file and see what happens.
>
> Cheers,
> Karl
>
> P.S. I checked leaprc.ff99SB, and CG also exist there as sp2, but I don't
> think the force field uses that atom type. Can anyone else comment?
>
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