[gmx-users] atomtype c3 not found

[Mark Abraham]

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


>
> 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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