[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found
Justin A. Lemkul
jalemkul at vt.edu
Sat Jun 18 00:14:01 CEST 2011
Ye Yang wrote:
> 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).
Well, if you try again with single precision and things work normally, please
file a bug report. Otherwise, it's just speculation that I doubt would be
necessarily associated with precision. Topology I/O should not be affected.
> 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?
>
You can still use genion, just don't have it update your .top file for you. I
suppose you could pick through your coordinate file, delete some waters, and
place ions manually, but there's no problem with genion actually carrying out
this operation. Just omit the topology update and do it yourself.
-Justin
> Thank you very much
>
> Best
> Wishes
>
> Ye
>
> 2011/6/16 Justin A. Lemkul <jalemkul at vt.edu <mailto: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 <http://vt.edu> | (540) 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
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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