First, please think carefully about why you want to use 06. I don't
need to know why. I just want to make sure you've thought about it.
Next, yes you can, but you need to do some things.
1. Download the 06 files from the website. Be sure to get all files
you need: .dat, .prep, leaprc, and, if linking to a protein .lib.
2. You need to add "SCEE=1.0 SCNB=1.0" to every dihedral entry in
Glycam_06.dat. See Glycam_06h.dat for an example of how. You need
this because you can no longer specify scee and scnb values in the md
input file.
Then, just use those parameter files as you normally would.
On Mon, Jan 14, 2013 at 2:54 AM, Subrata Paul <paul.subrata34.gmail.com> wrote:
> Dear Lachele,
>
> Actually, we want to use GLYCAM_06 in AMBER12 not GLYCAM_06h.
> Is it possible to use GLYCAM_06 in amber12 ?
>
>
> Very very Thanks
>
> On Sun, Jan 13, 2013 at 12:18 AM, Lachele Foley (Lists)
> <lf.list.gmail.com>wrote:
>
>> Urszula was correct, but if you need a more complete approach, you can use:
>>
>> source leaprc.GLYCAM_06h
>>
>> If curious, you can see the contents of $AMBERHOME/dat/leap/cmd for
>> the available leaprc files.
>>
>>
>> On Fri, Jan 11, 2013 at 11:32 PM, Subrata Paul <paul.subrata34.gmail.com>
>> wrote:
>> > Thanks
>> >
>> > But, we want to use ff99SB and GLYCAM_06.
>> > So, How we load GLYCAM_06 in amber12 ?
>> >
>> > On Fri, Jan 11, 2013 at 8:38 PM, Lachele Foley (Lists) <
>> lf.list.gmail.com>wrote:
>> >
>> >> We started versioning our releases to facilitate reproducibility.
>> >>
>> >> If you are simulating certain glycoproteins or want to use ff12SB, you
>> >> might need even more recent parameters. Get those files from
>> >> glycam.org/params
>> >>
>> >>
>> >> On Fri, Jan 11, 2013 at 5:27 AM, Urszula Uciechowska
>> >> <urszula.uciechowska.chem.umu.se> wrote:
>> >> > In Amber12 you have glycam_06h
>> >> > you can load it in leap by typing:
>> >> > params = lodamberparams GLYCAM_06h.dat
>> >> >
>> >> > /Urszula
>> >> >
>> >> > Urszula Uciechowska, Ph.D.
>> >> > Department of Chemistry
>> >> > Umeå University
>> >> > SE-901 87 Umeå, Sweden
>> >> > urszula.uciechowska.chem.umu.se
>> >> > ________________________________________
>> >> > Von: Subrata Paul [paul.subrata34.gmail.com]
>> >> > Gesendet: Freitag, 11. Januar 2013 11:03
>> >> > An: AMBER Mailing List
>> >> > Betreff: [AMBER] Glycam_06 in amber12
>> >> >
>> >> > Dear Amber User,
>> >> >
>> >> > Can we use GLYCAM_06 force field in amber12 ?
>> >> > If possible, How ?
>> >> > --
>> >> > *With Best Regards
>> >> > Subrata
>> >> > PhD Student
>> >> > Dept of Chemistry.
>> >> > IIT G
>> >> > *
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >>
>> >> --
>> >> :-) Lachele
>> >> Lachele Foley
>> >> CCRC/UGA
>> >> Athens, GA USA
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> >
>> > --
>> > *With Best Regards
>> > Subrata
>> > PhD Student
>> > Dept of Chemistry.
>> > IIT G
>> > *
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> *With Best Regards
> Subrata
> PhD Student
> Dept of Chemistry.
> IIT G
> *
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Jan 14 2013 - 08:30:03 PST
