<div dir="ltr"><div>Hi Sarbani,</div>
<div> </div>
<div>I think you should use "genion -random no" along with other options. </div>
<div> </div>
<div>Thanks, </div>
<div>Vignesh<br><br></div>
<div class="gmail_quote">On Fri, Sep 12, 2008 at 3:30 PM, sarbani chattopadhyay <span dir="ltr"><<a href="mailto:sarbani_c84@rediffmail.com">sarbani_c84@rediffmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<p> Hi everybody,<br> I want to place my counterions close to the charged amino acids. I am aware of <br>the fact that even if the counterions are randomly added yet they will eventually settle during <br>
equlibration. But still I will like to start with a structure that has counterions close to charged <br>residues. <br>I have been going through the archive and the manual but I could not figure out how to <br>disable the default option of "-random" while using the "genion" command.<br>
<br>Can anyone guide me through the command that is required to add counterions based on <br>potential so that the counterions are closed to the charged residues?<br><br>Thanks in advance<br>Sarbani <br></p><br><br>
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