[gmx-users] error while executing grompp

[Mark Abraham]

Justin A. Lemkul wrote:
> 
> Your ffcharmm.itp file lacks a necessary line at the very top:
> 
> #define _FF_CHARMM
> 
> Without this line, grompp does not know which force field you are using, 
> and hence everything breaks down when other .itp files are called.

On closer inspection, Chanchal's source at 
http://www.bioinf.uni-sb.de/RB/ is redistributing a not-fully-functional 
version of the results of my CHARMM conversion scripts. I believe such 
redistribution is not technically a breach of the GPL license under 
which I released those scripts (since my copyright extends to the 
scripts, but not to their results since I understand that these are not 
"derivative works"), but those files and the website don't acknowledge 
their origin. The pre-print journal article linked there does 
acknowledge my work suitably, however. I'll email them and ask for a 
suitable correction.

Mark

> -Justin
> 
> Chanchal wrote:
>> Hi,
>>   Attached are the top and itp file I am using. Please help me to fix 
>> the problem.
>> Thanks
>> Chanchal
>>
>>
>> On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul <jalemkul at vt.edu 
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>>     Chanchal wrote:
>>
>>         Hi All,
>>           I have downloaded pdb file and required .top and .itp file
>>         from the site http://www.bioinf.uni-sb.de/RB/ for DOPC
>>         simulation. Now when I execute the command
>>          grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o
>>         dopc.tpr -e ener.edr -t traj.trr I got the error " Fatal error:
>>         [ file tip3p.itp, line 42 ]:
>>         Atom index (1) in settles out of bounds (1-0).
>>         This probably means that you have inserted topology section
>>         "settles"
>>         in a part belonging to a different molecule than you intended to.
>>         In that case move the "settles" section to the right molecule.
>>         -------------------------------------------------------
>>
>>         Attached is the em.mdp file I am using. Please help me how to
>>         solve this problem.
>>
>>
>>     Please see here:
>>
>>     
>> http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds 
>>
>>
>>     The .mdp file is not the source of the problem; the topology is.  If
>>     you need more help, you'll have to post the relevant section.
>>
>>     -Justin
>>
>>         Thanks
>>         Chanchal
>>
>>
>>         
>> ------------------------------------------------------------------------
>>
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>>
>>     --     ========================================
>>
>>     Justin A. Lemkul
>>     Ph.D. Candidate
>>     ICTAS Doctoral Scholar
>>     Department of Biochemistry
>>     Virginia Tech
>>     Blacksburg, VA
>>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>     ========================================
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>>
>