[gmx-users] pb2gmx SS bond selection

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 18 12:36:27 CET 2012

pithevenet at free.fr wrote:
> Dear all,
> I'm using the option -ss to select the SS bonds I want to preserve when so problem occur with multiple bonds possible.
> The problem is that pdb2gmx asks me if I want to preserve the bound between an atom or not. It is very difficult to do this automatically.
> Is there a way to tell pdb2gmx which one I would like to preserve without using thoses question? Directly in the command line?


To do so requires you to know the order of a (potentially) large string of 
numbers before running the command, so it may or may not save you a whole lot of 
time, unless you're doing the exact same thing multiple times (which is 
unnecessary, since you'd be creating the same topology).  Basically, you'd have 
to run pdb2gmx to get the sequence of responses, by which point, you no longer 
need the scripted version.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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