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This often happens if the sodium ion is not called "NA+" in the
forcefield<br>
you have invoked. It might be "NA" or "Na+" - look at
ions.itp and see what the<br>
correct name for the sodium ion is for the force field you are choosing
and<br>
make sure it exactly matches the name you used in the topology
file. If you are using<br>
a forcefield not explicitly included in ions.itp then you should check
the force field<br>
non-bonded parameter file to get the exact name of the sodium
atom.<br><br>
Cheers,<br>
Alan<br><br>
<br><br>
<br>
<blockquote type=cite class=cite cite="">Date: Wed, 22 Aug 2007 15:02:30
+0530<br>
From: "vijay kumar hinge vijay"
<vijaybioinfo2@gmail.com><br>
Subject: [gmx-users] error regarding NA+ atom<br>
To: gmx-users@gromacs.org<br>
Message-ID:<br>
<x-tab> </x-tab>
<c91230fc0708220232g2b376c88o601eb1f906e35e3b@mail.gmail.com><br>
Content-Type: text/plain; charset="iso-8859-1"<br><br>
Respected sir/madem,<br>
i am using gromacs - 3.1.4 version on sunsolaris platform.i got
error at<br>
position restrain at grompp step ,telling dat NO SUCH MOLECULE
TYPE<br>
NA+(both are in caps).beofre dat the error which i got , ihv done
following<br>
steps<br>
1.first i hv excuted pdb2gmx command den i noted down the charge which
given<br>
as out put.charge is -1<br>
2.after editconf(-d 0.9),genbox ,energy minimization(grompp,mdrun)
i had<br>
manipulated da .top file by adding #include 'ions.itp,removed one
water<br>
molecloe from SOL and added NA+ 1 at da end of
topology file .<br>
den i got error after runing da grompp of position restrain ,and i
had<br>
changed pr.mdp file ,in that i was added da SOL,0.1,300 (temp)<br>
thanking u for ur patiency<br>
regards<br>
vijaya kumar hinge</blockquote>
<x-sigsep><p></x-sigsep>
<tt><font face="Courier New, Courier" size=2>graduate student -
Pappu Lab<br>
Center for Computational Biology<br>
Washington University School of Medicine<br>
700 S. Euclid<br>
St. Louis, MO 63105<br>
(314)-362-2080</font> </body>
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