The Amber ff99 force field is very old and has been replaced with newer,
more accurate models. I strongly advise that you should not use ff99.
Please see the section of the manual on force fields for a more complete
discussion.
On Mon, May 7, 2018, 6:19 AM roja rahmani <roja.rhmn.gmail.com> wrote:
> Because i want topology file which is compatible with AMBER99 ff in
> GROMACS.
> I can make the simple THR sequences just in order and its topology file
> with tleap,parmed,.. but i want its capped helical structure and it is so
> different in parameter,... as you know. Because of that i asked here to
> know if it is possible to make this structure directly in ambertools to be
> more trusted and compatible in next step?
>
> Regards
> -roja
>
> On Mon, 7 May 2018, 14:33 ABEL Stephane, <Stephane.ABEL.cea.fr> wrote:
>
> > Hi Roja,
> >
> > I do not know why you asked your question in the Amber Mailing list for a
> > problem "not" related to Amber (in particularly if you want to use after
> > GROMACS). That being said, to build a peptide with a defined number of
> AAs
> > and particular conformation you could use
> >
> > ProBuilder : http://nova.disfarm.unimi.it/probuilder.htm
> > PeptideBuilder a python script :
> > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3661355/
> >
> > and then use pdb2gmx, etc....
> >
> > Good luck
> >
> > Stéphane
> >
> >
> > ----------------------------------------------------------
> > Stéphane Abel, Ph.D.
> > Commissariat à l’Energie Atomique et aux Energies Alternatives
> > Centre de Saclay DSV/ISVFJ/SB2SM
> > Bat 528, Office 138C
> > Gif-sur-Yvette, F-91191 FRANCE
> > Phone (portable) : +33 6 49 37 70 60
> > ________________________________________
> > De : roja rahmani [roja.rhmn.gmail.com]
> > Envoyé : dimanche 6 mai 2018 15:29
> > À : AMBER Mailing List
> > Objet : Re: [AMBER] Poly amino acid helix form topology files
> >
> > I can't understand this part of manual, but all in all thank you so much.
> >
> > On Sun, 6 May 2018, 17:50 Carlos Simmerling, <
> carlos.simmerling.gmail.com>
> > wrote:
> >
> > > I don't have experience with gromacs setup. For Amber you should look
> in
> > > the Leap section of the manual at the impose command. You should also
> > > search the mailing list archive for leap impose.
> > >
> > > On Sun, May 6, 2018, 9:15 AM roja rahmani <roja.rhmn.gmail.com> wrote:
> > >
> > > > Would you please directly refer me to the exact page and manual.
> Which
> > > page
> > > > directly refer to this issue?
> > > > Then, i want its topology files for gromacs and not simulate in
> amber.
> > > >
> > > > Best
> > > > -roja
> > > >
> > > > On Sun, 6 May 2018, 17:31 Carlos Simmerling, <
> > > carlos.simmerling.gmail.com>
> > > > wrote:
> > > >
> > > > > You can use the impose command in leap to build a helical backbone.
> > See
> > > > the
> > > > > manual for details.
> > > > >
> > > > > On Sun, May 6, 2018, 2:53 AM roja rahmani <roja.rhmn.gmail.com>
> > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I want to have poly threonine(10 threonine) but in helix form and
> > > then
> > > > > add
> > > > > > NME and ACE add terminals. I draw it in PYMOL but there are some
> > > > problems
> > > > > > in structure which is not identified by amber.
> > > > > >
> > > > > > Is there any way to have this molecule in helux form directly in
> > > amber?
> > > > > And
> > > > > > extract its .prmtop aand .incprd file Would you please help me?
> > > > > >
> > > > > > Best regards
> > > > > > -roja
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 07 2018 - 05:30:03 PDT
