Thank you so much, what about poly amino acids? For example polyalanine? Is
this structure still standard?however residue should be standard .... and
ALA is..
Best
On Thu, 26 Apr 2018, 15:50 David A Case, <david.case.rutgers.edu> wrote:
> 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 Mon Apr 30 2018 - 04:00:02 PDT
