Dear Xavi,
The dat file for the 2004 glycam force field is included within version 8 of
Amber. Please see the amber website for details on how to obtain the latest
version of the software. The new 2004 glycam force field has been derived
for use with the standard 6-12 non bonded equation used in amber. However,
it has been parameterised for use WITHOUT the need for scaling 1-4
non-bonded interactions. Therefore, ensure you read section 2.7 of the amber
8 manual before using the Glycam 04 force field.
With regards to Glycam2000a you can use this with Amber 7 but you will need
to recompile sander to use a 10-12 term for the van der waals interactions.
Add "-DHAS_10_12" to the MACHINEFLAGS section of the machine file and then
recompile sander.
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Javier Perez Miron
> Sent: 17 March 2004 19:03
> To: amber.scripps.edu
> Subject: AMBER: About glycam2004
>
> Hi Amber community,
>
> I would like to know where I can find the .dat file about
> glycam 2004 Force
> Field. I want to use this Force Field. I have seen the Amber
> web page. There is
> a page where they talk about Glycam FF. There are many
> versions about this kind
> of FF. The current version parameters is in glycam_2000a.dat
> file(for AMBER 5).
> I would like to know if this FF can be used also in AMBER 7.
>
> Have a nice day!!
>
>
>
> Xavi Perez
>
> Chemoinformatic
> Universitat Autonoma de Barcelona
> Barcelona, Spain.
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Received on Tue Mar 23 2004 - 18:53:01 PST
