ahmet yıldırım wrote:
When I created em.tpr I got the followings notes:
*_NOTE 1 [file topol.top, line 52]:_*
System has non-zero total charge: -1.500000e+01
_*NOTE 2 [file topol.top]:*_
The largest charge group contains 11 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
then, I tried to add ions.
Neither of these notes is relevant to the problem at hand, although the second
means that some component of your topology is badly broken.
Just to be very clear, after rearranging your .gro and .top such that (1) they
match and (2) all solvent molecules are continuous, you have created a new .tpr
file and you're still getting an error from genion?
-Justin
Thanks
01 Nisan 2011 15:33 tarihinde Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> yazdı:
ahmet yıldırım wrote:
Dear users,
I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta.
...and hopefully did a complete re-parameterization of the nonsense
charges it gives.
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
That's an aside, completely unrelated to your actual problem, though.
genion -s em.tpr -o solvated.gro -nname Na -nn 15 -g em.log
select group:13
Fatal error:
The solvent group SOL is not continuous: index[984]=5334,
index[985]=5355
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/Documentation/Errors
You still haven't answered the second question I posed below. I
assume this "em.tpr" file has not been re-generated from a properly
continuous .gro and .top combination. If either were out of order
with respect to the other (i.e. changing the .top and not the .gro),
you would have gotten a fatal error from grompp when creating em.tpr.
-Justin
01 Nisan 2011 15:17 tarihinde Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>> yazdı:
ahmet yıldırım wrote:
I tried SOL 44453 but I still the same error
Are you using some index file that is specifying a discontinuous
water group? Have you properly re-created your genion input .tpr
file from this new topology?
-Justin
01 Nisan 2011 15:11 tarihinde Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>> yazdı:
On 1/04/2011 11:03 PM, ahmet yıldırım wrote:
Dear Dr. Mark,
I did you said but I have the same error. please
look at
attached file
topol.top:
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
SOL 185
SOL 143
SOL 44125
TRS 1
EDO 1
OK, well maybe it doesn't like different chunks of the
same
molecule
even when they're adjacent in order. Try "SOL 44453"
instead.
Mark
01 Nisan 2011 14:41 tarihinde Mark Abraham
<mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>>> yazdı:
On 1/04/2011 10:26 PM, ahmet yıldırım wrote:
Dear Justin,
I have Fatal Errror:The solvent group
Water is not
continuous. I look at gmx-users mailing list
search. I
also have the same problem.
You
said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
It is exactly what I said; you've proven
it. You have
solvent, ligand, then
solvent. To use genion (as the program
prints out
at the
prompt) you must have
a *continuous* group of solvent in order
to embed
ions. If
you re-arrange the
coordinate file and [molecules] section of the
topology,
you can achieve this.
How can I do the re-arrange you said? Can you
explain a
little bit?
You need a system topology whose molecules are
ordered such
that all the water is contiguous. That means the
order of the
names of molecule types in your [ molecules ]
section
of your
.top can have only one mention of water. Since the
order of
molecules in the coordinate file must match this
order, you
will need to physically reorder your [ molecules ]
section,
and the chunks of molecules in your coordinate
file.
Fortunately, you don't have to renumber those
atoms
in the
coordinate file.
Mark
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-- Ahmet YILDIRIM
-- ========================================
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> <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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Ahmet YILDIRIM
--
========================================
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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