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Hello,<br><p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2"><br>I
have conducted several runs in which I pull one peptide away from
another; however, the peptide being pulled gets visually “stretched”
out when viewing the trajectory in VMD and DSSP confirms this. I came
across this recent post
(<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-September/064621.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-September/064621.html</a>)
in which it was recommended to apply distance restraints and use
particle decomposition to solve the stretching problem.<br><br>I
tried this, but grompp keeps throwing this
error:<br><br>-------------------------------------------------------<br>Program
grompp, VERSION 4.5.4<br>Source code file: toppush.c, line:
1526<br><br>Fatal error:<br>[ file disres.itp, line 5 ]:<br>Atom
index (1583) in distance_restraints out of bounds (1-1578).<br>This
probably means that you have inserted topology section
"distance_restraints"<br>in a part belonging to a different
molecule than you intended to.<br>In that case move the
"distance_restraints" section to the right molecule.<br>For
more information and tips for troubleshooting, please check the
GROMACS<br>website at
<a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>-------------------------------------------------------<br><br>Here’s
the workflow I used:<br><br>1) Making indices<br>make_ndx –f
NPT.gro –o index.ndx<br>> a 1-789<br>> 19 a_1-1578 : 789
atoms<br><br>> a 790-1578<br>> 20 a_1579-3156: 789 atoms<br><br>>
name 19 Chain_A<br>> name 20 Chain_B<br><br>> 20 & a
CA<br><br>Copied index group 20 'a_1579-3156'<br>Found 208 atoms with
name CA<br>Merged two groups with AND: 1578 208 -> 104<br><br>21
a_1579-3156_&_CA : 104 atoms</font></font></p>
<p style="margin-bottom: 0cm"><br>
</p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2">Making
the distance restraint</font></font></p>
<p style="margin-bottom: 0cm"><br>
</p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2">genrestr
-f NPT.gro -o disres.itp -disre -n index.ndx</font></font></p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2">Select
a group: 21</font></font></p>
<p style="margin-bottom: 0cm"><br>
</p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2">3)
Then I added:</font></font></p>
<p style="margin-bottom: 0cm; text-decoration: none"><font style="font-size: 9pt" size="2"><font face="Courier New, monospace">#ifdef
POSRES_B</font></font></p>
<p style="margin-bottom: 0cm; background: transparent; line-height: 100%; text-decoration: none">
<font face="Courier New, monospace"><font size="2"><span style="background: transparent">#include
"disres.itp"</span></font></font></p>
<p style="margin-bottom: 0cm; background: transparent; line-height: 100%">
<font face="Courier New, monospace"><font size="2"><span style="background: transparent"><span style="text-decoration: none">#endif</span></span></font></font></p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2">after
the include statement for the position restraint file to the *.itp
file for the peptide being pulled</font></font></p>
<p style="margin-bottom: 0cm"><br>
</p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2">4)
Next I added “disre = simple” and “define -DDISRES to the MDP
setting</font></font></p>
<p style="margin-bottom: 0cm"><br>
</p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2">5)
Next, I run grompp as follows (after which I get the aforementioned warning):<br></font></font><br>
</p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2">grompp
-f PULL.mdp -c NPT.gro -p topol.top -n index.ndx -t NPTpbc.trr -o
PULL.tpr</font></font></p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2"><br>Initially
I use pdb2gmx -chainsep to tell GMX not to treat the two peptides as
1 molecule, and when the topologies are written for the peptides,
they both start at atom 1. It's obvious that the out of bounds
warning is due to an atom numbering issue (grompp doesn't realize
that atom 1583 = atom 5 when you renumber the second peptide starting at 1), but I've drawn a blank as to how to work around
this. </font></font>
</p>
<p style="margin-bottom: 0cm"><br>
</p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2">Any
suggestions will be greatly appreciated</font></font></p>
<p style="margin-bottom: 0cm"><br>
</p>
<p style="margin-bottom: 0cm"><font face="Courier New, monospace"><font size="2">Thanks!
<br></font></font><br>
</p>
<p style="margin-bottom: 0cm"><br>
</p>
<p style="margin-bottom: 0cm"><br>
</p>
<p style="margin-bottom: 0cm"><br>
</p>
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