[email protected] 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
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
