[gmx-users] convert amber topology and coordinates files into gromacs topology

[Pedro Lacerda]

Tammy,

ACPYPE may help you!

http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder

Best regards

2016-07-03 21:26 GMT-03:00 Ming Tang <m21.tang at qut.edu.au>:

> Dear list,
>
> I am studying glycoprotein. As amber is very slow on CPUs, I really want
> to do my simulations in gromacs. I found that gromacs has amber99sb.ff. So
> I want to convert amber topology and coordinates files into gromacs
> topology using Antechamber. My concerns are:
>
> 1)      amber16 has leaprc.protein.ff14SB now, then is it reliable to
> study my glycoprotein using amber99sb.ff in gromacs?
>
> 2)      If amber99sb.ff in gromacs is reliable, will the topology changing
> process using Antechamber affect the simulation results?
>
> Thank you,
> Tammy
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