[gmx-users] Tool for visualizing disulphide bonds

[Erik Lindahl]

Hi,

On Oct 13, 2007, at 6:12 PM, Yang Ye wrote:

> Program like VMD can draw extra bond. You need to get its manual  
> and code a line or two in TCL.
>
> Regards,
> Yang Ye
>
> On 10/14/2007 11:38 PM, van Bemmelen wrote:
>> Hi Ozge,
>>
>> I'm not sure what you mean by "visualization". But what about  
>> using VMD
>> for trajectory visualization and creating a representation that  
>> contains
>> only the sulphur atoms forming the disulphide bonds?
>>

The big caveat with disulphides is of course that they are covalent  
bonds, and therefore assigned in the topology (pdb2gmx uses input  
structure distances to determine whether to connect them). Even if  
the molecule would like to move apart and break them, they will be  
intact for the entire simulation since we put them there.

Cheers,

Erik