Hi
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"? Greetings Lara ----- Ursprüngliche Message ----- Von: Justin A. Lemkul <[email protected]> An: Lara Bunte <[email protected]>; Discussion list for GROMACS users <[email protected]> CC: 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 -- ======================================== Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
