Thanks for the suggestion, however, what is SOURCE3 in gaff.dat referring to? I don't see it defined
anywhere.
Sorry if it is too obvious, but I cannot find it :-(
Rebeca
> From: hannes.loeffler.stfc.ac.uk
> To: amber.ambermd.org
> Date: Fri, 13 Feb 2015 18:40:35 +0000
> Subject: Re: [AMBER] angles values in GAFF for alkynes
>
> Look at the end of that file for SOURCE3.
> ________________________________________
> From: Rebeca García Fandiño [regafan.hotmail.com]
> Sent: 13 February 2015 18:19
> To: amber.ambermd.org
> Subject: [AMBER] angles values in GAFF for alkynes
>
> Dear Amber users,
> Looking into the GAFF.dat file, I have noticed that the angles among c1-c1-c3 and c1-c1-ha are 177.99 and 178.38 respectively
>
> c1-c1-c3 56.4 177.99 SOURCE3 4 1.0065 1.1721
> c1-c1-ha 44.8 178.38 SOURCE3 41 1.6952 2.0683
>
> However, these angles should be 180. If we have, for example, an alkyne CH3-C=C-H (c3-c1-c1-ha), it should be linear, and both angles should be 180.
>
> Does anybody know why the values for these angles have been established to values different from 180?? Would it be any problem if they are changed to 180?
>
> Best wishes,
>
> Rebeca
>
> Dr. Rebeca Garcia
> Santiago de Compostela University
> Spain
>
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Received on Fri Feb 13 2015 - 11:00:03 PST
