[gmx-users] CHARMM36 Termini Topology Incomplete

João Rodrigues j.p.g.l.m.rodrigues at gmail.com
Mon May 4 23:43:45 CEST 2015

Hi Justin,

In order to solve the issue, I need to know exactly what you're doing -
> exact
> command and full pdb2gmx screen output, please.  Issues with missing
> parameters
> for neutral termini should have been fixed well over a year ago; you are
> using
> the latest ports, correct?  I released a new version last month.  If those
> files
> are giving you issues, I need to figure out what's going on.
> -Justin

I am using the latest port yes, April 2015, with Gromacs 5.0.4.

Here's the pastebin for the pdb2gmx command <http://pastebin.com/c2ubYrFg>.

Here's the pastebin for the grompp command. <http://pastebin.com/J22XMt7N>

Let me know what I can do to help you debug, or if I'm doing something

Cheers and thanks,


2015-05-04 21:43 GMT+02:00 João Rodrigues <j.p.g.l.m.rodrigues at gmail.com>:

> Hi all,
> I am trying to setup a simulation of a peptide with neutral termini, using
> the CHARMM36 port from the MacKerell lab. While pdb2gmx works well, grompp
> fails with several erros about missing parameters, e.g.:
> ERROR 1 [file topol.top, line 1225]:
>   No default U-B types
> ...
> ERROR 4 [file topol.top, line 1689]:
>   No default Proper Dih. types
> All these are related to the termini, whether I use CT2 or COOH, or NH2.
> Could I copy the missing parameters from the old CHARMM27.ff files? Or
> should I contact the developers directly? The default charged termini work
> fine.
> Or should I add the ACE/NMA caps in f.e. Pymol?
> Cheers,
> João

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