<HTML><BODY>Change name Cl to name CL and check name Na in forcefield you use (it could be NA).<br><br><br>11 декабря 2011, 17:30 от Mark Abraham <Mark.Abraham@anu.edu.au>:<br><blockquote style="border-left: 1px solid rgb(8, 87, 166); margin: 10px; padding: 0pt 0pt 0pt 10px;" class="mailru-blockquote"><div id="class_1323766146">
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On 11/12/2011 11:43 PM, yp sun wrote:
<blockquote type="cite" cite="mid:1323607388.74407.YahooMailClassic@web15604.mail.cnb.yahoo.com">
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<td style="font: inherit;" valign="top">The name of ion is
different when using different force field You can check
which field force you use and find out how Na and Cl ion
is written in this force field.<br>
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<br>
The molecule name is constant over all force fields in the 4.5
series of GROMACS, and the molecule name is all that genion cares
about. Atom and residue names might vary.<br>
<br>
Mark<br>
<br>
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Yeping Sun<br>
CAS Key Laboratory of Pathogenic Microbiology &
Immunology<br>
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES <br>
NO.1 Beichen West Road,Chaoyang District,Beijing
100101,china<br>
<br>
--- <b>11年12月11日，周日, Setare Jiji <i><a target="_blank" href="sentmsg?compose&To=jj.64fhony@yahoo.com" class="style_13236102210000000274moz-txt-link-rfc2396E"><jj.64fhony@yahoo.com></a></i></b>
写道：<br>
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发件人: Setare Jiji <a target="_blank" href="sentmsg?compose&To=jj.64fhony@yahoo.com" class="style_13236102210000000274moz-txt-link-rfc2396E"><jj.64fhony@yahoo.com></a><br>
主题: [gmx-users] No such moleculetype Na<br>
收件人: <a target="_blank" href="sentmsg?compose&To=gmx-users@gromacs.org" class="style_13236102210000000274moz-txt-link-abbreviated">gmx-users@gromacs.org</a><br>
日期: 2011年12月11日,周日,下午5:17<br>
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<td style="font-size: 10pt; font-family: arial;" id="yiv617815497drftMsgContent">Hi,<br>
Thanks for your responding.<br>
<br>
I checked my ions.itp file in which
file sodium and chlorine ions are as
Na and Cl form.<br>
<br>
Thus, I used genion as follows:<br>
<br>
genion -s ions.tpr -o
1AKI_solv_ions.gro -p topol.top
-nname Cl -nn 8 -pname Na<br>
<br>
Unfortunately, I encountered same
fatal error.<br>
<br>
any help will highly appreciated.<br>
<br>
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