[gmx-users] Atomtype:CB

[Mark Abraham]

> 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
http://wiki.gromacs.org/index.php/Parameterization.

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

Mark