[gmx-users]gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

[Ye Yang]

> 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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