[gmx-users] 11-cis retinal topology problem

Albert mailmd2011 at gmail.com
Sun Jul 7 08:58:53 CEST 2013

On 07/07/2013 03:18 AM, Justin Lemkul wrote:
> This problem can be solved by remembering to complete step 5 of 
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field. 
> As Mark notes, though, this issue is entirely separate from your 
> initial problem.
> -Justin

Hello Justin:

  thanks a lot for kind advices. This problem solved now. However, the 
grompp still have some problems:

  grompp_mpi -f em.mdp -c gmx.pdb -o em.tpr

source code gromacs-4.6.2/src/kernel/toppush.c, line: 726
Fatal error:
Unknown bond_atomtype NCH1

It is pretty strange, I already add NCH1 atom type in ffbonded.itp as 

[ bondtypes ]
; i    j    func    b0    kb
NCH1    CT2    1    0.149    284512.0
NCH1    HCR    1    0.1    359824.0
NCH1    CR15    1    0.132    410032.0

In the atomtypes.atp, I also have information:

NCH1    14.00700 ;    LYR

Why it still complained?

thank you very much


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