[gmx-users] pdb2gmx -ss option

[Mark Abraham]

On 16/01/12, pithevenet at free.fr wrote:

> 
> Dear all,
> 
> I'm using the old 3.3.3 version of gromacs and I try to use the -ss option of pdb2gmx to select interactively the ss bridge in my protein.
> 
> But I don't remark any change between using -ss option and not using it. The -inter option give me some interactive options such as lys or arg but not ss interactive selection.
> 
> Could you help me?
> 
> 

There are various possible reasons, including that the distance criterion is not met, or that your cysteine residues are in different soon-to-be moleculetypes. Unfortunately you haven't provided enough detailed description of your system or your pdb2gmx command line or its output for anyone to work with.
 
You should be sure to have a compelling scientific reason for wanting to use 3.3.3. Performance and useability are much higher with modern versions. 
 
Mark 
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