Francesco Pietra wrote:
Hello Sunny:
I had already generated a valid .itp file for my protein using
seq2itp. That .itp works for both the protein itself and the protein
graphically inserted into a bilayer. When I add graphically further
water it does not work any more. I thought there is something else
that manages water without putting it everywhere. That script does not
help.
In order to get a solution to your problem, I think you're going to have to
explain your methodology more clearly, including command lines and actual error
messages. How are you adding water "graphically"? Is genbox not working? Can
you not simply grep for the number of water molecules, i.e.:
grep W solvated.gro | wc -l
and use that number in the topology?
-Justin
thanks
francesco
On Wed, Oct 21, 2009 at 3:46 PM, sunny mishra <mishra.su...@gmail.com> wrote:
There is a seq2itp.pl script provided by martini folks in their
website. You can get it from there.
Sunny
On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra
<francesco.pie...@accademialucchese.it> wrote:
Hi:
I am looking for scripts that generate topology in coarse grained.
Thanks for indications.
francesco pietra
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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