[gmx-users] pb2gmx SS bond selection

[Justin A. Lemkul]

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?
> 

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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