On 8/11/2011 5:36 PM, cuong nguyen wrote:
Dear,
I created a 5 5 2 box containing 15 mibc and 15 decanol molecues by
using two comands:
/genbox -ci decanol.gro -nmol 15 -box 5 5 2 -o layer.gro -p decanol.top
genbox -cp layer.gro -ci decanol.gro -nmol 15 -box 5 5 2 -o box.gro -p
mibc.top/
The -ci value for this command would insert more decanol, not mibc.
then I filled this mixture by water to create other 5 5 10 box by
using comands:
/genbox -cp mix.gro -cs spc216.gro -o box1.g96 -p topol.top -box 5 5 10/
Where did mix.gro come from?
If you want to encourage people to help you, these commands should be
copied and pasted from your terminal (or the shell script you wrote so
that your procedure was self-documenting). Otherwise we've got no reason
to suppose your reported input and your reported output have any causal
relationship between them. The more things you filter through your head
each time, the more errors you will make - and that goes for more than
workflows for getting help! :)
the topol.top file is:
/#include "ffG43a1.itp"
#include "decanol.itp"
#include "mibc.itp"
; include water
#include "spce.itp"
[ system ]
MIBC and dec in water
[ molecules ]
dec 15
mibc 15
sol 7947./
then I ran the grompp comand: grompp -f input_min.mdp -o min.tpr -c
box1.g96 and the errors was
/Warning: atom name 2 in topol.top and box1.g96 does not match (CAC -
CAF)/
/Warning: atom name 3 in topol.top and box1.g96 does not match (CAE -
CAB)/
/Warning: atom name 4 in topol.top and box1.g96 does not match (CAG -
CAE)/
/Warning: atom name 5 in topol.top and box1.g96 does not match (CAI -
CAG)/
/Warning: atom name 6 in topol.top and box1.g96 does not match (CAK -
CAC)/
/Warning: atom name 7 in topol.top and box1.g96 does not match (CAJ -
OAD)/
/Warning: atom name 8 in topol.top and box1.g96 does not match (CAH -
HAN)/
/Warning: atom name 9 in topol.top and box1.g96 does not match (CAF -
CAA)/
/Warning: atom name 10 in topol.top and box1.g96 does not match (CAD -
CAF)/
/WARNING 1 [file topol.top, line 20]:/
/220 non-matching atom names/
/atom names from topol.top will be used/
/atom names from box1.g96 will be ignored/
/---------------------------------------------------
/
/Fatal error:/
/Too many warnings (2), grompp terminated./
/If you are sure all warnings are harmless, use the -maxwarn option./
/For more information and tips for troubleshooting, please check the
GROMACS/
/website at http://www.gromacs.org/Documentation/Errors /
Please help me to correct these errors.
The order of the [molecules] section of the grompp -p file must match
the order in the grompp -c file. The order of the atoms within the
[moleculetype] sections must likewise match the order in the grompp -c
file. Yours don't, for some reason. You will have to look at these
orderings and deduce what is wrong.
Mark
Thank you very much
best regards,
Cuong
2011/11/7 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
cuong nguyen wrote:
Dear,
Thanks a lot Justin. I created a box containing mixed solution
of 20 hexanol molecues and 20 octanol molecules in water.
However, when I run grompp and mdrun commands, gromacs noticed
errors with the topol.top file for this mixed system.
So please help me to create a suitable topol.top file to this
system.
No one can help you without knowing the exact errors that grompp
produced.
-Justin
Thanks a lot.
Best regards,
Cuong
2011/11/7 Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>>
Justin A. Lemkul wrote:
cuong nguyen wrote:
Dear,
I would like to create a solution of mix substances
(hexanol
and octanol) in water. I got top files and gro files of
these alcohols from PRODRG server. However I do not
know how
to mix these top file to create topol.top file for
this mixture.
Please read the tutorial:
http://www.gromacs.org/__Documentation/Tutorials#__Heterogeneous_Systems
<http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems>
Also possibly useful:
http://www.gromacs.org/__Documentation/How-tos/Mixed___Solvents
<http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents>
-Justin
-- ==============================__==========
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 <tel:%28540%29%20231-9080>
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981 <tel:%28%2B61%29%20452213981>
--
========================================
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
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Mobile: (+61) 452213981 <tel:%28%2B61%29%20452213981>
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