Re: [Fwd: counterion software]

From: bora erdemli (
Date: Mon Oct 11 2004 - 02:03:05 CDT

Hi all;

As we discussed earlier in the mailing list, there is
VMD plug in which name is 'autoionize' that can help

best regards

Bora Erdemli

--- Cetin Baloglu <> wrote:


Sorry all, I've just  seen Wat2ions .

thanks ,
Cetin Baloglu

-------- Original Message -------- Subject:
      counterion software Date:
Mon, 11 Oct 2004 07:51:56 +0300 From:
  Cetin Baloglu <>

Hi,I want to add some amount of chloride as counterion
to my protein file, before running with namd. To be
more effective , I don't want to do it manually. There
is a program for that purpose on site ,unfortunately
it works only for sodium ion. I checked the C file,
but couldn't find the variable to change sodium ion
charge so as to mimick a negative ion. Can you offer
me a script or a small program for that purpose.thanks
in advance.Cetin Baloglu
> begin:vcard
> fn:Cetin Baloglu
> n:Baloglu;Cetin
> org:Sabanci University;Biological Sciences &
> Bioengineering
> adr:;;MDBF Sabanci
> Universitesi;Tuzla;Istanbul;34956;Turkey
> email;
> title:IT Academic Support Assistant
> tel;work:+902164839000 int:2116
> url:
> version:2.1
> end:vcard

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