[gmx-users] Disulphur bridge parameters

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 10 12:42:45 CET 2011

On 10/11/2011 9:28 PM, alberto arrigoni wrote:
> Dear gromacs users,
> I am simulating a protein complex with a disulphur bridge. I put the 
> two chains in the same "moleculetype" definition, 

pdb2gmx does not read [moleculetype] definitions, it writes them.

> and through pdb2gmx I generate the disulfur bridge. When I checked the 
> .top file for angles and dihedral angles potential parameters I found 
> out that these fields were empty. I wonder why this happens, thanks!

As usual, providing your actual command lines and input would lead to 
you getting useful help sooner. As it is, I'll guess that you haven't 
used the specbond.dat mechanism (and/or pdb2gmx -ss option) 
appropriately. See manual section 5.6.7.


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