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On 5/11/2011 1:05 AM, kirubakaran palani wrote:
<blockquote
cite="mid:CAHo4-LPxdVQ1BefFrzM+0fv3+y3QM49yOAhOj_HpOKZ83MSPvQ@mail.gmail.com"
type="cite">Dear All<br>
<br>
Could any one help me to solve this error in gromacs 4.5.5
version. I am running dynamics on apo protein and the protein
shows negative charge of -6 (after choosing OPLS-AA force filed)
and when i was neutralizing the -6 with +6 and generating the
genion.tpr file there it shows "No such moleculetype NA+" error.
But the same protein was running with out any error message in
gromacs 4.0.7 version.<br>
</blockquote>
<br>
The naming convention has changed. See share/top/oplsa.ff/ions.itp<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAHo4-LPxdVQ1BefFrzM+0fv3+y3QM49yOAhOj_HpOKZ83MSPvQ@mail.gmail.com"
type="cite">
<br>
The error message was given below.<br>
<br>
Kindly rectify the problem<br>
=======================================================================================<br>
[student@localhost gro]$ grompp -f em.mdp -p topol.top -c
genion.gro -o genem.tpr<br>
<br>
<br>
Ignoring obsolete mdp entry 'cpp'<br>
<br>
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#<br>
Generated 332520 of the 332520 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 0.5<br>
Generated 332520 of the 332520 1-4 parameter combinations<br>
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'<br>
Excluding 2 bonded neighbours molecule type 'SOL'<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 4.5.5<br>
Source code file: toppush.c, line: 1987<br>
<br>
Fatal error:<br>
No such moleculetype NA+<br>
For more information and tips for troubleshooting, please check
the GROMACS<br>
website at <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
========================================================================================<br>
<br>
<br>
<br>
Regards<br>
<br>
Kirubakaran P<br>
<br>
<br>
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<br>
</blockquote>
<br>
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