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Dear Sir ,<br>
I used your CG parameters and gromacs V3.3&nbsp; to simulate protein
aggregation.&nbsp; And&nbsp; my command is : <br>
<font color="#ff0000">grompp_mpi_d -np 2&nbsp; -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>
#&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; BONDS:&nbsp;&nbsp; 1935<br>
#&nbsp; G96ANGLES:&nbsp;&nbsp; 2565<br>
#&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; IDIHS:&nbsp;&nbsp; 225<br>
#&nbsp;&nbsp;&nbsp;&nbsp; CONSTR:&nbsp;&nbsp; 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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; OTHER residues<br>
There are:&nbsp; 1170&nbsp;&nbsp;&nbsp; PROTEIN residues<br>
There are:&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 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="">&nbsp;
</span>-np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro<span
 style="">&nbsp; </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="">&nbsp;
</span>-np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro<span
 style="">&nbsp; </span>-o toypeptide.tpr<br>
</span></p>
<p class="MsoNormal" style="margin-left: 6pt; text-indent: -6pt;">____________________________________________________________________________________<br>
index.ndx&nbsp; :</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="">&nbsp;&nbsp; </span>1<span
 style="">&nbsp;&nbsp;&nbsp; </span>2<span style="">&nbsp;&nbsp;&nbsp;
</span>3<span style="">&nbsp;&nbsp;&nbsp; </span>4<span style="">&nbsp;&nbsp;&nbsp; </span>5<span
 style="">&nbsp;&nbsp;&nbsp;
</span>6<span style="">&nbsp;&nbsp;&nbsp; </span>7<span style="">&nbsp;&nbsp;&nbsp; </span>8<span
 style="">&nbsp;&nbsp;&nbsp;
</span>9<span style="">&nbsp;&nbsp; </span>10<span style="">&nbsp;&nbsp; </span>11<span
 style="">&nbsp;&nbsp;
</span>12<span style="">&nbsp;&nbsp; </span>13<span style="">&nbsp;&nbsp; </span>14<span
 style="">&nbsp;&nbsp;
</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="">&nbsp; </span>16<span
 style="">&nbsp;&nbsp; </span>17<span style="">&nbsp;&nbsp;
</span>18<span style="">&nbsp;&nbsp; </span>19<span style="">&nbsp;&nbsp; </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>&nbsp;</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>&nbsp;</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?&nbsp; By the&nbsp; way, I test&nbsp;
other cases&nbsp; in your website&nbsp; and I didn't&nbsp; get&nbsp; any&nbsp; error&nbsp; message .<br>
Best regards <br>
&nbsp;<br>
Wang Yeng-tseng <br>
<br>
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