[gmx-users] atomtype c3 not found

[Mark Abraham]

On Mon, Apr 7, 2014 at 1:48 PM, Monoj Mon Kalita <mon.123chem at gmail.com>wrote:

> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Mon, 7 Apr 2014 12:50:21 +0200
> > From: Mark Abraham <mark.j.abraham at gmail.com>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Cc: Discussion list for GROMACS users
> >         <gromacs.org_gmx-users at maillist.sys.kth.se>
> > Subject: Re: [gmx-users] atomtype c3 not found
> > Message-ID:
> >         <
> > CAMNuMAR+26NRUYM85KvoUKrgKFn4nr6BHfvwFBujtxhTNuCJ6A at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > On Mon, Apr 7, 2014 at 11:22 AM, Monoj Mon Kalita <mon.123chem at gmail.com
> > >wrote:
> >
> > > Dear users
> > >
> > > I am trying to simulate a ligand and protein in POPC. I have calculated
> > the
> > > ligand paramteres using the generalized amber force field (GAFF)  and
> > now I
> > > am trying to simulate the ligand-protein system with amber99sb-ildn ff.
> >  I
> > > have added the lines in the topology file like this
> > >
> > >
> > > ; Include forcefield parameters and compound atomtypes
> > > #include "amber99sb-ildn.ff/forcefield.itp"
> > > #include "ligand-non-bonded.itp"
> > >
> > > ; Include chain topologies
> > > #include "topol_Protein.itp"
> > >
> > > ; Include water topology
> > > #include "amber99sb-ildn.ff/spc.itp"
> > > ;Include ion parameters
> > > #include "amber99sb-ildn.ff/ions.itp"
> > >
> > > ;Include compoud
> > > #include "ligand.itp"
> > >
> > > [ system ]
> > > ; Name
> > > protein
> > >
> > > [ molecules ]
> > > Protein
> > > SOL
> > > MOL
> > >
> > > But the grompp is not reading the ligand parameters. It is showing the
> > > error 'atomtype c3 not found'.
> > >
> >
> > That kinda means what it says. ligand-non-bonded.itp is supposed to be
> > doing that definition, so have a look inside it and decide who is not
> > matching who, and why.
> >
> > Mark
> >
> >
> > Yes, I know that. But, my question was is there any other method to
> define
> these new atom types as they are not implemented in amber99sb-ild.ff of
> gromacs.


No, that's what you intended to ask. ;-) "Suggest... how to solve this
issue" actually asked us to guess what the real problem with atom
definition was.


> I tried to define them in ffnonbonded.itp file. Then that error
> doesn't appear, but after performing genion step I get a broken molecule,
> means gromacs ignores the connections of my ligand.
>

No, that means mdrun doesn't take pains to write confout.gro output with
molecules made whole with respect to PBC. trjconv will fix that, however.

Mark


>
>
> > >
> > > These are the atomtypes in my ligand file from GAFF
> > >
> > >  c3       c3          0.00000  0.00000   A     3.39967e-01
> 4.57730e-01
> > ;
> > > 1.91  0.1094
> > >  n3       n3          0.00000  0.00000   A     3.25000e-01
> 7.11280e-01
> > ;
> > > 1.82  0.1700
> > >  hc       hc          0.00000  0.00000   A     2.64953e-01
> 6.56888e-02
> > ;
> > > 1.49  0.0157
> > >  hn       hn          0.00000  0.00000   A     1.06908e-01
> 6.56888e-02
> > ;
> > > 0.60  0.0157
> > >
> > > which are already in the ligand-non-bonded.itp file.
> > >
> > > Can anybody suggest me, how to solve this issue. I have seen this issue
> > in
> > > the archive, but didn't find much information in it.
> > >
> > > http://comments.gmane.org/gmane.science.biology.gromacs.user/41031
> > >
> > >
> > > with regards
> > >
> > > Mon
> > > --
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