Justin A. Lemkul wrote:
Smiruthi Ramasubramanian wrote:
Justin,
I tried to use an index file with atom numbers of the water molecules
in the required volume.
But when I try to ionize the box, I get this error:
Fatal error:
The solvent group SOL is not continuous: index[717]=21689,
index[718]=21696
This makes sense, but is there a way get around this?
The fundamental requirement of genion is that the solvent is continuous
in the coordinate file. If that's not true, genion won't work. If you
have continuous solvent, a valid index group within that section should
work just fine.
Another option is to write your own script that replaces water molecules with
the desired ion type; it should be relatively simple to randomly choose water
molecules to replace based on simple coordinate criteria. Updating the topology
would have to be done manually, and you'd have to find a way to generate a
syntactically correct coordinate file after making replacements, but that is
also fairly simple I/O with, for example, Perl.
-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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