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

[Ye Yang]

Thank you for your suggestions.
I have checked the topology file with vim, and it looks pefectly, also, the
only problem happens when I use genion. One thing that might be possible is
that I use the double precision version of gromacs, because when I solve it
in water, the written of topology file looks weired(like I showed).
What do you mean by work-around? You mean just manually change some water
molecules in topology file and coordinate file into ions? Will the program
recognize something like CL, NA? Or can I just add ions to the system and
solve it in water?

Thank you very much

Best
Wishes

Ye

2011/6/16 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> Ye Yang wrote:
>
>> 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'
>>
>>
> Something doesn't match up here - the command backs up temp.top, but then
> complains it can't find SOL in topol.top.  Either genion is looking at the
> wrong file or your command is somehow wrong.
>
>
>  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.
>>
>>
> If removal of the JZ4 line relieves the problem, perhaps there's a problem
> with that line, i.e. the line ending?  What type of system are you using?
>  Sometimes Windows line endings cause problems.  Always use a plain text
> editor and use dos2unix to process text files if you're on Windows.
>
> Otherwise, the work-around is to not have genion work on the topology.
>  Make the corrections yourself.  Simple addition of ions and subtraction of
> water molecules is trivial.
>
> -Justin
>
>
>  Can someone help me with this problem?
>>
>> Thank you all very much.
>>
>> Ye Yang
>>
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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