[gmx-users] grompp Unkown bond_atomtype C2

Lara Bunte lara.bunte at yahoo.de
Wed May 16 14:05:24 CEST 2012


in my .rtp file I wrote in the [ atoms ] block

C2   CN1A    0.7481   1 

but in the atomtypes.atp file I wrote

CN1A    12.01100

So I declared it. So what do you mean with "such an atom type doesn't exist"?


----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 13:22 Mittwoch, 16.Mai 2012
Betreff: Re: [gmx-users] grompp Unkown bond_atomtype C2

On 5/16/12 3:56 AM, Lara Bunte wrote:
> Hi
> After:
> pdb2gmx -f mymol.pdb -water tip3p
> editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro
> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
> I typed:
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> where em.mdp is my energy minimization file and I got:
> Fatal error:
> Unknown bond_atomtype C2
> What is here the problem? All atom types should be declared by me, I guess.

You're making use of an atom type called "C2" in some bonded interaction, but 
such an atom type doesn't exist.  You need to define it.



Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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