[gmx-users] how to make topol.top file for mixed solution
cuong nguyen
nvcuong68 at gmail.com
Tue Nov 8 07:36:34 CET 2011
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*
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*
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.
Thank you very much
best regards,
Cuong
2011/11/7 Justin A. Lemkul <jalemkul at 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 <jalemkul at vt.edu <mailto:jalemkul at 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>
>>
>> <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>
>> <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> | (540) 231-9080
>> <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<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
>>
>>
>
> --
> ==============================**==========
>
> 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<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
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