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 <jalem...@vt.edu
<mailto:jalem...@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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