[gmx-users] how to fit parameters for terminal residues in amber99sb-ildn?

[sang eun jee]

Dear Yoochan

Thank you very much for sharing useful information.I realized that this
topic is more related to how to describe termini more realistically in case
of specific system. My system is simplified model of the complicated
realistic system. I will take into account those points to my research.

Best Regards,

Sangeun Jee

On Mon, Apr 6, 2015 at 2:16 PM, yoochan <yuchan.m at gmail.com> wrote:

> Dear Sangeun,
>
> Sorry, I misunderstood your question.
>
> As you mentioned, currently AMBER Force Field doesn't support -NH2, -COOH
> parameters about terminal group.
>
> I have no idea and I think it won't be easy, unless you are not going to
> make new force fields using Antechamber(AMBER TOOL).
>
> But why don't you check previous case?
> http://archive.ambermd.org/201003/0382.html <
> http://archive.ambermd.org/201003/0382.html>
>
> Yoochan.
>
> > On Apr 6, 2015, at 11:34 PM, sang eun jee <sangeunjee at gmail.com> wrote:
> >
> > Hi Yoochan
> >
> > Thanks for your reply.
> > Actually my question was not specifically stating what I was really
> curious.
> >
> > I know how to modify the library in AMBER99sb-ildn forcefield and pdb2gmx
> > worked when I modified forcefield library in a right way. However, my
> goal
> > is to simulate system with NH2 and COOH termini, not to simulate with
> > capping termini via NME or other capping materials. What I wondered was,
> If
> > I would like to include parameters for GLY with NH2 termini and HYP with
> > COOH in amber99sb-ildn library, I need to know specific parameter values
> > for those residues.
> >
> > So, the question is, how can I derive parameters of GLY with NH2 termini
> > once I know the parameters of the GLY residue at the center of the
> chan(N-H
> > termini) and parameters of GLY with NH3 termini? Is there any specific
> rule
> > to derive the parameters for specific termini?
> >
> > Thank you very much,
> >
> > Sangeun Jee
> >
> > On Fri, Apr 3, 2015 at 9:54 PM, yoochan <yuchan.m at gmail.com> wrote:
> >
> >> Dear Sangeun,
> >>
> >> Did you try 'pdb2gmx' using your structure file?
> >>
> >> I checked NME and NHE are in the AMBER99sb-ildn forecefield.
> >>
> >> So, if pdb2gmx doesn't work, you can draw NME and NHE using molecular
> >> viewer and then change residue/atom name to NME and NHE.
> >>
> >>
> >> Yoochan
> >>
> >>
> >>
> >>> On Apr 4, 2015, at 7:01 AM, sang eun jee <sangeunjee at gmail.com> wrote:
> >>>
> >>> Dear  gromacs users
> >>>
> >>> Hello. I have question how to decide terminal residue forcefield and
> put
> >>> them in library?
> >>>
> >>> I am using AMBER99sb-ildn forcefield in gromacs. Not like gromos or
> opls
> >>> forcefield, amber forcefield treat termini in its own way and current
> >>> version only works with NH3+ and COO-. I would like to termini as a
> >> neutral
> >>> status, NH2 and COOH and would like to modify forcefield to include
> this
> >>> specific termini data.
> >>>
> >>> To decide charges and parameters to describe specific termini, is there
> >> any
> >>> way to decide parameters based on non-terminal residue database? When I
> >>> looked at NGLY and GLY from animoacids.rtp,  I could not find out
> >> specific
> >>> rules.
> >>>
> >>> Thank you very much.
> >>>
> >>> Sangeun Jee
> >>> --
> >>> Post Doctoral Researcher
> >>> School of Materials Science and Engineering
> >>> Georgia Institute of Technology
> >>> --
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> >
> >
> >
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> > Georgia Institute of Technology
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-- 
Post Doctoral Researcher
School of Materials Science and Engineering
Georgia Institute of Technology