On Wed, Apr 25, 2018, roja rahmani wrote:
>
> I'm beginner in amber. I want to add NME and ACE terminals to zwitterionic
> amino acid like threonine and then make an input topology file for
> GROMACS(.itp file) to be compatible with (AMBER99 ff in) GROMACS.
To build in Amber, use something like this in tleap:
source leaprc.protein.ff14SB # current force field in the "Amber99" tradition
pep = sequence { ACE THR NME }
saveamberparm pep capthr.parm7 capthr.rst7
(This is a "standard", not a "non-standard", peptide. At any point
inside tleap, you can type "help" or "help <command>" to get
instructions.)
To convert to gromacs, follow the instructions here:
http://ambermd.org/parmed_gromacs.html
A note: GROMACS seems to have a potential called "ffamber99". You
almost certainly don't want to use that. Look at your gromacs
documentation to find out how to access more modern Amber protein force
fields. (Or, consider running your simulation in Amber itself.)
....dac
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Received on Thu Apr 26 2018 - 04:30:04 PDT
