AMBER Archive (2009)

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

From: Shubhra Gupta (shubhg_at_iiar.res.in)
Date: Wed Jun 17 2009 - 05:33:50 CDT

Instead of leaprc.ff03 try to source leaprc.gaff.

Shubhra

On Wed, Jun 17, 2009 at 2:09 PM, Sergey Samsonov <
sergeys_at_biotec.tu-dresden.de> wrote:

> 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
>
>
>
>
>
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