> Hi, everyone: > 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 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html > I met some trouble in adding ion. > Each time when I use genion, it shows: > > Will try to add 0 NA ions and 6 CL ions. > Select a continuous group of solvent molecules > Group 0 ( System) has 33046 elements > Group 1 ( Protein) has 1693 elements > Group 2 ( Protein-H) has 1301 elements > Group 3 ( C-alpha) has 163 elements > Group 4 ( Backbone) has 489 elements > Group 5 ( MainChain) has 653 elements > Group 6 ( MainChain+Cb) has 805 elements > Group 7 ( MainChain+H) has 815 elements > Group 8 ( SideChain) has 878 elements > Group 9 ( SideChain-H) has 648 elements > Group 10 ( Prot-Masses) has 1693 elements > Group 11 ( non-Protein) has 31353 elements > Group 12 ( Other) has 15 elements > Group 13 ( JZ4) has 15 elements > Group 14 ( Water) has 31338 elements > Group 15 ( SOL) has 31338 elements > Group 16 ( non-Water) has 1708 elements > Select a group: 15 > Selected 15: 'SOL' > Number of (3-atomic) solvent molecules: 10446 > > Processing topology > > Back Off! I just backed up temp.top to ./#temp.top.3# > > ------------------------------------------------------- > Program genion_d, VERSION 4.5.4 > Source code file: gmx_genion.c, line: 285 > > Fatal error: > No line with moleculetype 'SOL' found the [ molecules ] section of file > 'topol.top' > > I checked my topology file and it looks fine: > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > ; Include water topology > #include "gromos43a1.ff/spc.itp" > > ; Include ligand topoloty > #include "drg.itp" > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include topology for ions > #include "gromos43a1.ff/ions.itp" > > [ system ] > ; Name > > Protein > [ molecules ] > ; Compound #mols > Protein_chain_A 1 > JZ4 1 > SOL 10446 > > 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. > > 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. > > Can someone help me with this problem? > > Thank you all very much. > > Ye Yang > > >
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