[gmx-users] itp file for aminoacids

[Mark Abraham]

Hi,

THR is parameterized for being part of a protein, yes.

Mark

On Mon, 30 Oct 2017 17:42 rose rahmani <rose.rhmn93 at gmail.com> wrote:

> i think ive got it now, you mean standalone aminoacids are inappropriate
> for now,BUT they are usable in concept of proteins(as its particle),am i
> right?
>
> On Mon, Oct 30, 2017 at 7:38 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > As I think Justin said a few days ago, force fields are typically
> > parameterized for proteins, so THR means the dipeptide moiety, not e.g.
> the
> > zwitterionic one. The latter would need many of the atoms to have
> different
> > charges. It's essentially a different molecule, and one which the force
> > field designers might or might not have felt important to target. If you
> > need the standalone amino acids, then you should choose your force field
> > (plus perhaps topology+parameter generation strategy) with that in mind,
> > rather than assuming that any particular force field is appropriate, and
> > then trying to make your square problem fit in that round hole.
> >
> > Mark
> >
> > On Mon, Oct 30, 2017 at 5:04 PM rose rahmani <rose.rhmn93 at gmail.com>
> > wrote:
> >
> > > yes of course
> > >
> > > On Mon, Oct 30, 2017 at 7:27 PM, R C Dash <rcdash0910 at gmail.com>
> wrote:
> > >
> > > > can you please upload your PDB file?
> > > >
> > > > On Mon, Oct 30, 2017 at 11:41 AM, rose rahmani <
> rose.rhmn93 at gmail.com>
> > > > wrote:
> > > >
> > > > > if it is included,so why AMBER doesnt identify amino acids like
> THR?
> > > > > error is such 'X' residuetype is not found in residue topology
> > > > > database?!!!!
> > > > > i dont know what is the problem?
> > > > >
> > > > > thanks for your attention
> > > > >
> > > > > On Mon, Oct 30, 2017 at 6:25 PM, R C Dash <rcdash0910 at gmail.com>
> > > wrote:
> > > > >
> > > > > > use https://atb.uq.edu.au/index.py /
> > > > > > http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg / or
> > > > > > http://swissparam.ch/
> > > > > > or http://vienna-ptm.univie.ac.at/  for .itp file
> > > > > > All amino acids are identified bybby AMBER force field. If you
> > there
> > > is
> > > > > > some modification like methylated lysine you have to creat a lib
> > file
> > > > and
> > > > > > use it in tleap AMBERTools.
> > > > > >
> > > > > > On Mon, Oct 30, 2017 at 10:48 AM, Tasneem Kausar <
> > > > > > tasneemkausar12 at gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > You only need a pdb file for amino acids/proteins. pdb2gmx in
> > > gromacs
> > > > > > does
> > > > > > > the job of making itp.
> > > > > > >
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> > > > > > >
> > > > > > > On Mon, Oct 30, 2017 at 8:11 PM, rose rahmani <
> > > rose.rhmn93 at gmail.com
> > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > > hello
> > > > > > > >
> > > > > > > > how can i make an .itp file for amino acids?
> > > > > > > > which amino acids is identified in AMBER forcefield?
> > > > > > > > --
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