[gmx-users] problems with gromacs preprocessor

[Justin A. Lemkul]

There is no need to post three times in five minutes.  If someone has advice, 
they will attend to your post in due time.

This issue is commonly reported.  Making haphazard changes to your topology is a 
bad idea.  Please search the list archive (available through the interface at 
the Gromacs site), and consult the following:

http://www.gromacs.org/Documentation/Errors

-Justin

Asmaa Elsheshiny wrote:
> Dear All,
> 
>  when I want to use grompp program 
>  grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr
> 
> I got the following error message
> 
> Fatal error:
> [ file "spc.itp", line 41 ]:
>              Atom index (1) in settles out of bounds (1-0)
> 
> So I tried to modify the topology file by  removing the following
> 
> ; Include water topology
> #include "spc.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> 
> ; Include generic topology for ions
> #include "ions.itp"
> 
> Since there is no needs also ions.itp , because I didnot add any ions to the structure. Is this right?
> 
> Finally, I tried to use grompp again with the modified topology file. I gety a different error message 
> 
> Fatal error:
> No such moleculetype SOL 
> 
> I donot know why SOL (water) didnot recognized by grompp !!!!!!
> 
> How can I fix these problems ?????????????????
> 
> Regards,
> Asmaa_______________________________________________
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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