Chanchal wrote:
Hi Justin,
I have corrected the ffcharmm.itp file. But I am still getting the
error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
processing topology...
Generated 0 of the 595 non-bonded parameter combinations
-------------------------------------------------------
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1273
Fatal error:
[ file topol.top, line 3879 ]:
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.
-------------------------------------------------------
Well, then I'm out of ideas. Your files work for me; I can successfully produce
a .tpr file using a basic EM .mdp file. Have you validated your installation
using the test set? Have you made any modifications to the standard tip3p.itp file?
-Justin
Thanks
Chanchal
On Tue, Aug 25, 2009 at 5:06 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Chanchal wrote:
Hi Justin,
Sorry, I attached the wrong file. Attached is the correct file.
There is a space after #define:
#define _FF_CHARMM
Your file has #define_FF_CHARMM.
-Justin
Thanks
Chanchal
On Tue, Aug 25, 2009 at 4:56 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Chanchal wrote:
Hi Justin,
I am still getting the error message : Back Off! I just
backed
up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Generated 0 of the 595 non-bonded parameter combinations
-------------------------------------------------------
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1273
Fatal error:
[ file topol.top, line 3879 ]:
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.
-------------------------------------------------------
As you said I added the line #define_FF_CHARMM in
ffcharmm.itp.
Attached
The #define line is not present in that file. Take care to
use the
right files when you've made changes.
-Justin
is the file.
Thanks
Chanchal
On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> 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.
-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>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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>
<http://vt.edu> <http://vt.edu>
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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> <http://vt.edu>
<http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
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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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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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