[gmx-users] carbohydrate forcefield in gromacs

Sai Kumar Ramadugu sramadugu at gmail.com
Thu Nov 1 17:02:58 CET 2012

As far as I know,
Glycam06 (AMBER) force field is not included in gromacs4.5.5.
If you want you can use amb2gmx.pl script that is available online or from
Erin Sorin's website at CSU @ Long Beach.

Remember that if you want to use GLYCAM06, its better to use AMBER ff99SB
or ff03 or the recent ff12 or ff12SB.
And in case you are using it, know that AMBER uses mixed scaling. So you
have to follow my earlier posts where I asked Chris Neale about the mixed
scaling and also read his paper in Biopolymers (Chris correct me if I am

Also in the end do zero step minimization in gromacs and in amber and check
the values are correct to 3rd or 4th decimals.
I did this exercise and it works. But painful!!


On Thu, Nov 1, 2012 at 10:16 AM, Sanku M <msanku65 at yahoo.com> wrote:

> Hi,
>   Is carbohydrate forcefield in Charmm or Amber included in gromacs4.5.5
> topology folders ?
> Sanku
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