[gmx-users] atomtype c3 not found

[Monoj Mon Kalita]

>
>
> ------------------------------
>
> 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:
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> 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. 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.


> >
> > 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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