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--></style></head><body lang=EN-IN link=blue vlink="#954F72"><div class=WordSection1><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></div></body></html>