John Ladasky wrote:
I am starting to write my own turnkey scripts to automate GROMACS (v
4.5.4) work flow. Many of the GROMACS commands, such as pdb2gmx and
genion, have interactive options by default, meaning that you manually
enter information when the program runs.
In the tutorials, we are taught to invoke pdb2gmx from the command line
using certain arguments which name input and output files. But then, we
choose our force field from a numbered menu inside pdb2gmx. However, if
you know the name of the force field (these names SHOULD be listed
somewhere!), you can use the "-ff" argument when you call pdb2gmx from
the shell. For example, "-ff gromos45a3". Then you do not have to
manually enter anything.
I am looking for a corresponding option for genion. Genion offers a
numbered menu to ask you which group of atoms you wish to use for ion
replacements. The groups that most of us would want to use are the
"Water" or "SOL" groups. With the files that I'm working with right
now, these pop up as groups #12 and #13, respectively. But they needn't
always be numbered this way, if the user has altered the standard .ndx
file.
Is there an argument that one can supply to genion from the command
prompt which will select the replacement group automatically, as "-ff"
selects a force field for pdb2gmx? I have the v. 4.5.4 manual. I do
not see the argument (pp. 273-4). I hope that it exists, and that it is
just undocumented.
Groups can be chosen by name, and passed via 'echo' like other commands. See
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts. Thus
you can use something like
echo SOL | genion -s topol.tpr
-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
========================================
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