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

[sang eun jee]

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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-- 
Post Doctoral Researcher
School of Materials Science and Engineering
Georgia Institute of Technology