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 <jalem...@vt.edu <mailto:jalem...@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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