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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