[gmx-users] how to make topol.top file for mixed solution
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Nov 8 07:51:05 CET 2011
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 <jalemkul at vt.edu <mailto: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> <mailto: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>
>
>
> 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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>
>
> --
> Nguyen Van Cuong
> PhD student - Curtin University of Technology
> Mobile: (+61) 452213981 <tel:%28%2B61%29%20452213981>
>
>
>
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