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Hi,<br>
<br>
It is not the problem of your command line. It is related to how index
file is used with grompp. In general, there are pre-defined groups -
protein, non-protein, protein-H, etc; and there are user-defined
groups. In your case, Protein1 and TOYPEP are both user-defined groups.
So did you miss anything in the tutorial/example? Read the manual more
carefully to understand how grompp works. This list just tries to help
any user but not spoon-feed.<br>
<br>
Regards,<br>
Yang Ye<br>
<br>
On 10/24/08 3:19 PM, wang wrote:
<blockquote cite="mid:49017719.5070100@nchc.org.tw" type="cite">Dear
Sir ,<br>
I used your CG parameters and gromacs V3.3 to simulate protein
aggregation. And my command is : <br>
<font color="#ff0000">grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro
-p
aggre.top -o aggre.trp<br>
<font color="#000000">The error message is :<br>
<font color="#ff0000">double-checking input for internal
consistency...<br>
Velocities were taken from a Maxwell distribution at 300 K<br>
renumbering atomtypes...<br>
converting bonded parameters...<br>
# BONDS: 1935<br>
# G96ANGLES: 2565<br>
# IDIHS: 225<br>
# CONSTR: 900<br>
Walking down the molecule graph to make shake-blocks<br>
initialising group options...<br>
processing index file...<br>
Analysing residue names:<br>
Opening library file /opt/gromacs//share/gromacs/top/aminoacids.dat<br>
There are: 76048 OTHER residues<br>
There are: 1170 PROTEIN residues<br>
There are: 0 DNA residues<br>
Analysing Protein...<br>
Analysing Other...<br>
<br>
-------------------------------------------------------<br>
Program grompp_mpi_d, VERSION 3.3.3<br>
Source code file: readir.c, line: 798<br>
<br>
Fatal error:<br>
Group Protein1 not found in indexfile.<br>
Maybe you have non-default goups in your mdp file, while not using the
'-n' option of grompp.<br>
In that case use the '-n' option.</font><br>
<br>
But I tried your example case "A toy peptide in water" , I still got
the same error .<br>
My command is : <br>
</font></font>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">1.grompp_mpi_d<span style="">
</span>-np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro<span
style=""> </span>-n index.ndx -o toypeptide.tpr</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">2.grompp_mpi_d<span style="">
</span>-np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro<span
style=""> </span>-o toypeptide.tpr<br>
</span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;">____________________________________________________________________________________<br>
index.ndx :</p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;">
</p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">[ prot_sort ]</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US"><span style=""> </span>1<span
style=""> </span>2<span style="">
</span>3<span style=""> </span>4<span style=""> </span>5<span
style="">
</span>6<span style=""> </span>7<span style=""> </span>8<span
style="">
</span>9<span style=""> </span>10<span style=""> </span>11<span
style="">
</span>12<span style=""> </span>13<span style=""> </span>14<span
style="">
</span>15</span><span style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US"><span style=""> </span>16<span
style=""> </span>17<span style="">
</span>18<span style=""> </span>19<span style=""> </span>20</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
--------------------------------------------------------------------------------------------------------------------------------------------------------<br>
The error message :<br>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">Walking down the molecule graph to
make
shake-blocks</span><span style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">initialising group options...</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">processing index file...</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">-------------------------------------------------------</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">Program grompp_mpi_d, VERSION <st1:chsdate
year="1899" month="12" day="30" islunardate="False" isrocdate="False"
w:st="on">3.3.3</st1:chsdate></span><span style="color: red;"
lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">Source code file: readir.c, line: 798</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">Fatal error:</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">Group TOYPEP not found in indexfile.</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">Maybe you have non-default goups in
your mdp file,
while not using the '-n' option of grompp.</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;"><span
style="color: red;" lang="EN-US">In that case use the '-n' option.</span><span
style="color: red;" lang="EN-US"><o:p></o:p></span></p>
<br>
<br>
Sir, could you tell me how to fix the problem? By the way, I test
other cases in your website and I didn't get any error message .<br>
Best regards <br>
<br>
Wang Yeng-tseng <br>
<br>
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