[gmx-users] Unknown bond_atomtype

[Mark Abraham]

Hi,

You've specified a type for your atom in [atoms] and elsewhere a bond that
uses it. Grompp has to find parameters for a bond between those two types,
etc. Choose existing types ;-)

Mark

On Wed, 17 Feb 2016 17:27 Nash, Anthony <a.nash at ucl.ac.uk> wrote:

> Hi all,
>
> As per a previous email (cross linking two peptide chains), I¹ve created a
> brand new crosslink (think disulphide bond) residue from scratch. I have
> defined it in all the files necessary (.rtp, residuetypes, specbond,
> atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no
> problems.
>
> Unfortunately when I run grompp (5.0.4) I get the following error:
>
> Fatal error:
> Unknown bond_atomtype MN1 <‹‹ first atom in my new residue
>
>
> At first I thought my topology might be pointing to the wrong forcefield,
> but I¹ve checked and double checked:
>
> #include "/usr/local/gromacs/share/gromacs/top/amber99sb.ff/forcefield.itp"
> #include "modic.itp"
> ;#ifdef POSRES
> ;#include "posre.itp"
> ;#endif
>
> [ system ]
> ; Name
> MODIC with glycine terminal ends
>
> [ molecules ]
> ; Compound        #mols
> MODIC             1
>
>
> I¹m going to take a guess at what the problem is. Each of the atoms in the
> residue was derived from scratch.Therefore, they have a completely new
> type. I wasn¹t feeling very creative with my naming convention so the atom
> name and the atom type are identical e.g.,
>
> ;MODIC crosslink
> [ MOD1 ]
>  [ atoms ]
> ; NAME    TYPE    CHARGE      NUMBER
> MN1     MN1     -0.3640         1
> MC1     MC1     0.0358          2
> MC15    MC15    0.4871          3
> Š
>
> Š
>
> Will this have confused grompp?
>
> Many thanks
> Anthony
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
>
>
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