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<div class="moz-cite-prefix">The developer list is for question
about development. Please ask on the gmx-users list.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2020-02-19 19:08, Mansi Porwal wrote:<br>
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<p class="MsoNormal">I am using <b>gromacs version 2016.3</b>.
I created an ice structure using GenIce Program and used tip5p
water model. My output was a .gro file. Now I want to create
the topology file of this ice structure. When I am using the
command <b>gmx pdb2gmx -f ice5_Ih.gro -o ice5_Ihnew.gro</b>
and using <b>charmm36-mar2019 force field</b> I am getting
the error “<b>Residue HO5 not found in residue topology
database”</b>. I even tried converting the .gro file I got
from GenIce to pdb and then using that pdb for pdb2gmx but it
showed the same error. After this I tried making my own
topol.top file.</p>
<p class="MsoNormal">My topol.top file is as follows</p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal">;; The main Gromacs topology file </p>
<p class="MsoNormal">;;</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">; Include forcefield parameters</p>
<p class="MsoNormal">#include
“charmm36-mar2019.ff/forcefield.itp</p>
<p class="MsoNormal">#include “toppar/tip5p.itp”</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">[system]</p>
<p class="MsoNormal">; Name</p>
<p class="MsoNormal">Icebox</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">[ molecules ]</p>
<p class="MsoNormal">; Compound #mols</p>
<p class="MsoNormal">Sol 7943</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">And then when I am running a gmx grompp
command for enery minimization using this topol.top file I am
getting the error </p>
<p class="MsoNormal"><b>Fatal error:<o:p></o:p></b></p>
<p class="MsoNormal"><b>Syntax error- File tip5-p.itp, line 6<o:p></o:p></b></p>
<p class="MsoNormal"><b>Last line read:<o:p></o:p></b></p>
<p class="MsoNormal"><b>‘[ moleculetype ]’<o:p></o:p></b></p>
<p class="MsoNormal"><b>Invalid error for directive molecule
type.<o:p></o:p></b></p>
<p class="MsoNormal">So can you please tell me what is wrong in
my topol.top file or any other method to generate topology
file.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Regards,</p>
<p class="MsoNormal">Mansi Porwal</p>
<p class="MsoNormal">M.Sc. Chemistry </p>
<p class="MsoNormal"><o:p> </o:p></p>
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