[gmx-users] Membrane protein MD Simulation

[Mark Abraham]

Behnoush Zare wrote:
> Thanks Yanzi,Thanks Mark,
> for your very usefull points,
> 
> I have another pdb2gmx running on thr protein.pdb with ffgmx force filed(matching with lipid.itp).
> Also I have removed the including ffG43a1 from the lipid.itp and then running grompp. The new errors are:
> 
> ERROR 1 [file "popc.itp", line 3]:
>   Incorrect number of atomtypes for dihedral (1 instead of 2 or 4)
> 
> Fatal error:
> Bonded/nonbonded atom type '1' not found!
> 
> I have read the chapter 5 of the manual but I dont have any idea about these errors.
> Could you please tell me what are these errors and what should I do to pass this step?

Well, neither do we, because we can't see line 3. However, from memory 
Table 5.1 or 5.2 will point out the different formats you can use for a 
dihedral interaction.

I suspect something else is quite badly wrong, however, because line 3 
is very early in a file for a dihedral to be being defined.

Mark