[gmx-users] itp file for aminoacids

[Mark Abraham]

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.
> > > > >
> > > > > <https://www.avast.com/sig-email?utm_medium=email&utm_
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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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