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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