[gmx-users] pdb2gmx -ss option

pithevenet at free.fr pithevenet at free.fr
Mon Jan 16 11:23:04 CET 2012

Thank you for your response.

I use 3.3.3 version because it's this one which is installed on the cluster, and that is difficult to change it without causing any bug and a reviewing is in process for the webservice. So change it now should be difficult.

To be able to select cysteins with the -ss option, the distance criterion must be met? In fact, my purpose was to get closer cystein that not met this creterion. But it seems to be not the best solution.

Thank you


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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