[gmx-users] itp file for aminoacids

[rose rahmani]

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.
> > > > > >
> > > > > > <https://www.avast.com/sig-email?utm_medium=email&utm_
> > > > > > source=link&utm_campaign=sig-email&utm_content=webmail>
> > > > > > Virus-free.
> > > > > > www.avast.com
> > > > > > <https://www.avast.com/sig-email?utm_medium=email&utm_
> > > > > > source=link&utm_campaign=sig-email&utm_content=webmail>
> > > > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> > > > > >
> > > > > > 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?
> > > > > > > --
> > > > > > > Gromacs Users mailing list
> > > > > > >
> > > > > > > * Please search the archive at http://www.gromacs.org/
> > > > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > > > >
> > > > > > > * Can't post? Read http://www.gromacs.org/
> Support/Mailing_Lists
> > > > > > >
> > > > > > > * For (un)subscribe requests visit
> > > > > > >
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > > or
> > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > >
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at http://www.gromacs.org/
> > > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > > or
> > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>