You can use 06 in amber12, but make sure you have SCEE and SCNB
entries in the parameter (.dat) file and that there are corresponding
sections in the prmtop file. Otherwise, the 1-4 scalings will be
wrong, and in amber12 you can no longer add them via the input file.
I don't recall when that change happened, but those entries weren't in
the original 06 files.
Before AMBER12, all the non-EP glycam leaprc's were called "06". So,
look inside that file to see which specific parameter file is being
called. It might not be plain 06.
There might be changes in some of the other parameters (bond, angle,
etc.). There weren't many. You just need to go through the
documentation and see if the changes apply to your situation. Look in
the prmtop file for the atom types in your system and see if any
changes apply. If any change involves atom types that are not in your
molecule, then that change will not affect you.
On Thu, Dec 27, 2012 at 6:03 AM, Subrata Paul <paul.subrata34.gmail.com> wrote:
> I have used a disaccharides with 06 force field with amber10. Actually,
> Now, I want to use that force filed with with amber12.
> Is it possilble ?
>
> Again, I tried to save the prmtop file with both 06 and 06h, I have found
> no change in charge.
> Is it will change the other like bond, dihedral ete ?
>
> thanking you
> subrata
>
>
>
>
> On Thu, Dec 27, 2012 at 12:53 PM, Lachele Foley (Lists)
> <lf.list.gmail.com>wrote:
>
>> Sorry I didn't answer earlier at the other address. Deadlines, plumbing,
>> etc...
>>
>> There are differences between 06 and 06h. In fact, there is now an
>> 06h-1. The latter might be important if you have a glycan attached to
>> a protein. To understand the changes, you would need to read the
>> documentation for all the releases in between. The docs are all here:
>> glycam.org/params
>>
>> If a PDB worked for 06, it should work for 06h.
>>
>> The changes would be in the force field. In most situations, 06h (and
>> 06h-1) should perform better than earlier versions.
>>
>>
>>
>> On Thu, Dec 27, 2012 at 1:10 AM, Subrata Paul <paul.subrata34.gmail.com>
>> wrote:
>> > Dear, Sir/Maam
>> >
>> > Previously, We are using GLYCAM_06 force field for a carbohydrate with
>> > AMBER10,
>> > but Now I want to use AMBER12, which have GLYCAM_06h.
>> >
>> > 1. Is there any difference between GLYCAM_06 and GLYCAM_06h?
>> >
>> > 2. Can we use that same PDB for carbohydrate with GLYCAM_06h in AMBER12?
>> >
>> > 3. Is it make some changes to the molecule?
>> >
>> > Wishing you a very Christmas
>> > Subrata
>> >
>> > --
>> > *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 Thu Dec 27 2012 - 09:00:05 PST
