<div dir="ltr"><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div dir="ltr">Hi, everyone:<br> I am a new user of Gromacs, and I am running through the tutorial. When I am trying to run the ligand-receptor binding tutorial from<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html</a><br>
I met some trouble in adding ion. <br> Each time when I use genion, it shows: <br><br>Will try to add 0 NA ions and 6 CL ions.<br>Select a continuous group of solvent molecules<br>Group 0 ( System) has 33046 elements<br>
Group 1 ( Protein) has 1693 elements<br>Group 2 ( Protein-H) has 1301 elements<br>Group 3 ( C-alpha) has 163 elements<br>Group 4 ( Backbone) has 489 elements<br>Group 5 ( MainChain) has 653 elements<br>
Group 6 ( MainChain+Cb) has 805 elements<br>Group 7 ( MainChain+H) has 815 elements<br>Group 8 ( SideChain) has 878 elements<br>Group 9 ( SideChain-H) has 648 elements<br>Group 10 ( Prot-Masses) has 1693 elements<br>
Group 11 ( non-Protein) has 31353 elements<br>Group 12 ( Other) has 15 elements<br>Group 13 ( JZ4) has 15 elements<br>Group 14 ( Water) has 31338 elements<br>Group 15 ( SOL) has 31338 elements<br>
Group 16 ( non-Water) has 1708 elements<br>Select a group: 15<br>Selected 15: 'SOL'<br>Number of (3-atomic) solvent molecules: 10446<br><br>Processing topology<br><br>Back Off! I just backed up temp.top to ./#temp.top.3#<br>
<br>-------------------------------------------------------<br>Program genion_d, VERSION 4.5.4<br>Source code file: gmx_genion.c, line: 285<br><br>Fatal error:<br>No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top'<br>
<br>I checked my topology file and it looks fine:<br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre.itp"<br>#endif<br><br>; Include water topology<br>#include "gromos43a1.ff/spc.itp"<br>
<br>; Include ligand topoloty<br>#include "drg.itp"<br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>
#endif<br><br>; Include topology for ions<br>#include "gromos43a1.ff/ions.itp"<br><br>[ system ]<br>; Name<br><br>Protein<br>[ molecules ]<br>; Compound #mols<br>Protein_chain_A 1<br>JZ4 1 <br>
SOL 10446<br><br>One thing that might happen is in the genion source file, I read through it, and the problem either happens in loading the line to buf2, or in the gmx_strcmp(buf2,"SOL"), since clearly the SOL_line is -1 aftermath.<br>
<br>The other thing I tried is to remove the ligand JZ4 part in both topology and coordinates file, and in this case, it works perfectly for adding ion. But in this way, I do not know how to insert my ligand into the system since it might collide with solvent.<br>
<br>Can someone help me with this problem?<br><br>Thank you all very much.<br><br>Ye Yang<br><br><br></div>
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