[gmx-users] Atomtype:CB

Mark Abraham mark.abraham at anu.edu.au
Fri Jul 27 01:48:53 CEST 2007

> Hello users,
>   I found a problem similar to one described in the mailing
> list. The problem occurs in grompp wherein it says
> unrecognized atom type CB. As suggested in the mailing list
> the problem arises when in a ligand protein system the
> ligand is prepared using the PRODRG server GROMOS87 format
> and the protein is prepared in some other FF..in my case
> 43a1(GROMOS96)..when i prepared my protein using the -ff gmx
> flag (gmx Gromacs Forcefield (a modified GROMOS87)) grompp
> did not have any problems. My question is that is there a
> way to prepare the ligand in 43a1 format so that when i run
> grompp the relevant input files are is the same desired
> format. Thanks in advance

If you're going to refer to previous mailing list discussions, please
prvoide a URL to the discussion you found in your search so we know what
you're talking about.

You should not mix and match force fields, see

ffgmx is deprecated and should not be used for new simulations.


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