[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>
>> >
>>
>>    ==============================**__==========
>>
>>    --     gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>    http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>>
>>    <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >
>>    Please search the archive at
>>    http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>>
>>    <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>
>> before posting!
>>    Please don't post (un)subscribe requests to the list. Use the www
>>    interface or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >.
>>    Can't post? Read http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>>
>>    <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >
>>
>>
>>
>>
>> --
>> 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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



-- 
Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111108/37ee822d/attachment.html>


More information about the gromacs.org_gmx-users mailing list