[gmx-users] pdb2gmx -ss option

Mark Abraham mark.abraham at anu.edu.au
Mon Jan 16 11:10:35 CET 2012

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. 
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