Hi Justin,<br> 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#<br>checking input for internal consistency...<br>processing topology...<br>Generated 0 of the 595 non-bonded parameter combinations<br>
<br>-------------------------------------------------------<br>Program grompp_d, VERSION 4.0.5<br>Source code file: toppush.c, line: 1273<br><br>Fatal error:<br>[ file topol.top, line 3879 ]:<br>Atom index (1) in settles out of bounds (1-0).<br>
This probably means that you have inserted topology section "settles"<br>in a part belonging to a different molecule than you intended to.<br>In that case move the "settles" section to the right molecule.<br>
-------------------------------------------------------<br><br>Thanks<br>Chanchal<br><br><br><div class="gmail_quote">On Tue, Aug 25, 2009 at 5:06 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Chanchal wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Justin,<br>
Sorry, I attached the wrong file. Attached is the correct file.<br>
</blockquote>
<br></div>
There is a space after #define:<br>
<br>
#define _FF_CHARMM<br>
<br>
Your file has #define_FF_CHARMM.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks<br>
Chanchal<div class="im"><br>
<br>
<br>
On Tue, Aug 25, 2009 at 4:56 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Chanchal wrote:<br>
<br></div><div><div></div><div class="h5">
Hi Justin,<br>
I am still getting the error message : Back Off! I just backed<br>
up mdout.mdp to ./#mdout.mdp.2#<br>
checking input for internal consistency...<br>
processing topology...<br>
Generated 0 of the 595 non-bonded parameter combinations<br>
<br>
-------------------------------------------------------<br>
Program grompp_d, VERSION 4.0.5<br>
Source code file: toppush.c, line: 1273<br>
<br>
Fatal error:<br>
[ file topol.top, line 3879 ]:<br>
Atom index (1) in settles out of bounds (1-0).<br>
This probably means that you have inserted topology section<br>
"settles"<br>
in a part belonging to a different molecule than you intended to.<br>
In that case move the "settles" section to the right molecule.<br>
-------------------------------------------------------<br>
<br>
As you said I added the line #define_FF_CHARMM in ffcharmm.itp.<br>
Attached<br>
<br>
<br>
The #define line is not present in that file. Take care to use the<br>
right files when you've made changes.<br>
<br>
-Justin<br>
<br>
is the file.<br>
Thanks<br>
Chanchal<br>
<br>
<br>
On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
Your ffcharmm.itp file lacks a necessary line at the very top:<br>
<br>
#define _FF_CHARMM<br>
<br>
Without this line, grompp does not know which force field you are<br>
using, and hence everything breaks down when other .itp files are<br>
called.<br>
<br>
-Justin<br>
<br>
Chanchal wrote:<br>
<br>
Hi,<br>
Attached are the top and itp file I am using. Please<br>
help me to<br>
fix the problem.<br>
Thanks<br>
Chanchal<br>
<br>
<br>
On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>>> wrote:<br>
<br>
<br>
<br>
Chanchal wrote:<br>
<br>
Hi All,<br>
I have downloaded pdb file and required .top and<br>
.itp file<br>
from the site <a href="http://www.bioinf.uni-sb.de/RB/" target="_blank">http://www.bioinf.uni-sb.de/RB/</a> for DOPC<br>
simulation. Now when I execute the command<br>
grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p<br>
topol.top -o<br>
dopc.tpr -e ener.edr -t traj.trr I got the error "<br>
Fatal<br>
error:<br>
[ file tip3p.itp, line 42 ]:<br>
Atom index (1) in settles out of bounds (1-0).<br>
This probably means that you have inserted<br>
topology section<br>
"settles"<br>
in a part belonging to a different molecule than you<br>
intended to.<br>
In that case move the "settles" section to the right<br>
molecule.<br>
-------------------------------------------------------<br>
<br>
Attached is the em.mdp file I am using. Please<br>
help me how to<br>
solve this problem.<br>
<br>
<br>
Please see here:<br>
<br>
<a href="http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds" target="_blank">http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds</a><br>
<br>
The .mdp file is not the source of the problem; the<br>
topology<br>
is. If<br>
you need more help, you'll have to post the relevant<br>
section.<br>
<br>
-Justin<br>
<br>
Thanks<br>
Chanchal<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>><br>
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-- ========================================<br>
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Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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