Try the "strip" command. Strip out the ions and then do
your "closest" command.
--Niel
________________________________________
From: Bruno Rodrigues [bbrodrigues.gmail.com]
Sent: Thursday, August 04, 2011 5:02 PM
To: AMBER Mailing List
Subject: [AMBER] 1st shell WITH solvent in ptraj
Dear all,
something very strange is happening with a ptraj command I am running.
Basically, I want to generate a .pdb with the 1st solvation shell with and
without counterions.
So I made some tests and found out a way to do that. But since I made these
tests, no matter which script I write, I ALWAYS keep the counterions in my
.pdb.
for example, the following command:
trajin 1D20_wat_tip4pewmd9_center_short.binpos 6 6 1
solvent byres :39-99999
closestwater 166 :1-20 first
trajout 1st_shell.pdb pdb
from 1-20 is my DNA. From 21-38 I have conterions. Then it should count only
the water molecules?
But it is inserting the ions, no matter their distance, no matter what I
do.....
the output of the command is enclosed.
Another thing, at some point in the past I also set up
closestwater 1 :21-38 first
in the ptraj command, to account for the ions, and I realized that since
then it keeps getting the ions, no matter this command is present. does it
make sense? If not, why does it keep the 18 ions (even far from the DNA) on
my pdb?
thank you in advance
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Thu Aug 04 2011 - 17:00:02 PDT
