For example this is what David advised me to do for normal THR THR...
structure.
source leaprc.protein.ff14SB # current force field in the "Amber99"
tradition
pep = sequence { ACE THR NME }
saveamberparm pep capthr.parm7 capthr.rst7 ....then use parmed for make
topology file for GROMACS.
As i couldn't understand how build helical structure by impose command in
AMBER, i tried to build this structure by Peptide builder software and make
it capped in AMBER. So i want to load the .pdb file in AMBER and then add
NME and ACE to it.
On Wed, 9 May 2018, 15:26 Juan Eiros, <j.eiros-zamora14.imperial.ac.uk>
wrote:
> Hi,
>
> Indeed you can. Page 203 of the Amber18 manual
> (http://ambermd.org/doc12/Amber18.pdf) has information on how to do it.
>
> Cheers
>
> Juan
>
>
> El 09/05/2018 a las 11:40, roja rahmani escribió:
> > Hi,
> >
> > I'm beginner in AMBER.
> > How can i add NME and ACE terminals to peptide(it's manually builded, not
> > in AMBER).
> > Would you please hrlp me?
> >
> > Regards
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed May 09 2018 - 05:30:03 PDT
