<div>Dear Gmx Users,</div>
<div> </div>
<div>I have built my system which includes a tube and a protein. I represented my tube as carbon atoms using Charmm27 ff. I processed pdb2gmx for a tube and protein togehter and divide it into two itp files including it in my topoloy file:</div>
<div> </div>
<div><span lang="EN">
<p>; Include forcefield parameters</p>
<p>#include "./charmm27mod.ff/forcefield.itp"</p>
<p>; Include tube topology</p>
<p>#include "Tubes.itp"</p>
<p>; Include Position restraint of Tube</p>
<p>#ifdef POSRES_T</p>
<p>#include "posreTubes.itp"</p>
<p>#endif</p>
<p>; Include Protein topology</p>
<p>#include "Protein.itp"</p>
<p>; Include Position restraint of Protein</p>
<p>#ifdef POSRES_P</p>
<p>#include "posreProtein.itp"</p>
<p>#endif</p>
<p>; Include Position restraint file</p>
<p>#ifdef POSRES</p>
<p>#include "posreALL.itp"</p>
<p>#endif</p>
<p>; Include water topology</p>
<p>#include "./charmm27mod.ff/tip3p.itp"</p>
<p>#ifdef POSRES_WATER</p>
<p>; Position restraint for each water oxygen</p>
<p>[ position_restraints ]</p>
<p>; i funct fcx fcy fcz</p>
<p>1 1 1000 1000 1000</p>
<p>#endif</p>
<p>; Include topology for ions</p>
<p>#include "./charmm27mod.ff/ions.itp"</p>
<p>[ system ]</p>
<p>; Name</p>
<p>Protein in water</p>
<p>[ molecules ]</p>
<p>; Compound #mols</p>
<p>Protein_chain_X 1</p>
<p>Tubes_chain_X 1</p>
<p>Then I added 23000 water molecules and trying to process grompp in order to replace water molecules with ions obtained errors:</p>
<p>ERROR 1 [file Protein.itp, line 6]:<br> Expected a molecule type name and nrexcl</p>
<p><br>ERROR 2 [file Protein.itp, line 7]:<br> Expected a molecule type name and nrexcl<br></p>
<p>.....</p>
<p> </p>
<p>My Protein.itp file is copied from topol.top file and 1st lines look like:</p><span lang="EN">
<p>[ moleculetype ]</p>
<p>; Name nrexcl</p>
<p>Protein_chain_X 3</p>
<p>; residue 1009 MET rtp MET q 0.0</p>
<p>1009 NH2 1009 MET N 1009 -0.96 14.007 ; qtot -0.96</p>
<p>1010 H 1009 MET HT1 1010 0.34 1.008 ; qtot -0.62</p>
<p>1011 H 1009 MET HT2 1011 0.34 1.008 ; qtot -0.28</p>
<p>1012 CT1 1009 MET CA 1012 0.19 12.011 ; qtot -0.09</p>
<p>1013 HB 1009 MET HA 1013 0.09 1.008 ; qtot 0</p>
<p>1014 CT2 1009 MET CB 1014 -0.18 12.011 ; qtot -0.18</p>
<p>1015 HA 1009 MET HB1 1015 0.09 1.008 ; qtot -0.09</p>
<p>1016 HA 1009 MET HB2 1016 0.09 1.008 ; qtot 0</p>
<p>1017 CT2 1009 MET CG 1017 -0.14 12.011 ; qtot -0.14</p>
<p>1018 HA 1009 MET HG1 1018 0.09 1.008 ; qtot -0.05</p>
<p>1019 HA 1009 MET HG2 1019 0.09 1.008 ; qtot 0.04</p>
<p>1020 S 1009 MET SD 1020 -0.09 32.06 ; qtot -0.05</p>
<p>1021 CT3 1009 MET CE 1021 -0.22 12.011 ; qtot -0.27</p>
<p>1022 HA 1009 MET HE1 1022 0.09 1.008 ; qtot -0.18</p>
<p>1023 HA 1009 MET HE2 1023 0.09 1.008 ; qtot -0.09</p>
<p>1024 HA 1009 MET HE3 1024 0.09 1.008 ; qtot 0</p>
<p>1025 C 1009 MET C 1025 0.51 12.011 ; qtot 0.51</p>
<p>1026 O 1009 MET O 1026 -0.51 15.999 ; qtot 0</p></span>
<p>Do you have any clue what is wrong?</p>
<p>Then another Error starting from the 1st (1009) atom of my protein:</p>
<p>Atom index (1009) in bonds out of bounds (1-0).<br>This probably means that you have inserted topology section "bonds"<br>in a part belonging to a different molecule than you intended to.<br>In that case move the "bonds" section to the right molecule.<br>
</p>
<p>My tube is not connected with a protein. Should I turn off CMAP? Will it affect it?</p>
<p>Thank you,</p>
<p>Steven</p></span></div>