[gmx-users] Using Glycam forcefield and amber forcefield together

[Mark Abraham]

Hi,

Things can also be unstable because the starting configuration is too wrong
for the model at normal step sizes, even when the model is valid, because
the forces produce movements that are too large for the time step. You
should also consider being super gentle as you start equilibration, e.g. no
constraints and tiny time step.

Mark

On Sun, 19 Jun 2016 10:17 bharat gupta <bharat.85.monu at gmail.com> wrote:

> Dear Gromacs Users,
>
> I have been trying to simulate a docked complex of cellobiohydrolase with
> cellotriose for the past 1 week. I have derived the parameters of
> ellotriose from ATB server and with these parameters I am getting LINCS
> warning at the nvt equilibration step, which I assume is due to the bad
> parameterization of the ligand i.e. cellotriose. I also tried simulating
> the ligand alone in vaccum and I end with the same LINCS warning at nvt
> step. So, I thought to change my strategy by using the GLYCAM06 forcefield
> for cellotriose and  Amber ff99SB force field for the protein, but I am not
> able to understand how to do that? Any help in this regard would be highly
> appreciated.
>
> --
> *Best Regards*
> Bharat
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