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Dear Users:
<div><br>
</div>
<div>Summary:</div>
<div>
<div><font color="#222222" face="arial, sans-serif" size="2">I believe that there is some problem in the residue numbering routine that is used by editconf and trjconv</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">that exists at least in 4.5.3 and 4.5.5, but not in 4.0.7, and that this is somehow related to the ACE residue.</font></div>
</div>
<div><font color="#222222" face="arial, sans-serif" size="2"><br>
</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">Details:</font></div>
<div>I have a system with two peptides, water, and ions. Residues are numbered consecutively in the initial .gro file </div>
<div>(verified by running editconf -resnr 1). The problem is that when I use grompp to generate a .tpr file and then </div>
<div>use editconf -f my.tpr -o out.gro I get a .gro file with residues that are not listed consecutively (same thing if I use</div>
<div>trjconv to extract a .gro from a .xtc file with this .tpr).</div>
<div><br>
</div>
<div>I tested this in gromacs 4.5.5 and 4.5.3. The forcefield is either Amber99sb or OPLS-AA/L. Each peptide is capped </div>
<div>(starts with ACE and ends with NME).</div>
<div><br>
</div>
<div>If I order them as protein1, protein2, water, ions in the .gro and .top then the .gro that I extract from the .tpr</div>
<div>has residue numbers that run from 1-14 (first peptide), then again 1-15 (second peptide), and continue as </div>
<div>16-1413 (water), 1414-1439 (ions).</div>
<div><br>
</div>
<div>If I reorder to put ions first, then I get residue numbers that run from 16-41 (ions), 1-14 (first peptide), </div>
<div>1-15 (second peptide), 42-1439 (water).</div>
<div><br>
</div>
<div>In each case, however, the output from gmxdump provides molblock fields that are in the correct order.</div>
<div><br>
</div>
<div>I wonder if there could be something about the ACE residue in the force field that is causing this </div>
<div>strange behaviour? I've used a single capped peptide before, but never more than one and the ACE residue</div>
<div>has always come first in my previous work.</div>
<div><br>
</div>
<div>Here is the molblock information from gmxdump in the setup in which I put the ions before the first peptide:</div>
<div><br>
</div>
<div><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">topology:</span></div>
<div><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> name="MD"</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #atoms = 4652</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> molblock (0):</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> moltype = 0 "NA"</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #molecules = 15</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #atoms_mol = 1</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> molblock (1):</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> moltype = 1 "CL"</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #molecules = 11</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #atoms_mol = 1</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> molblock (2):</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> moltype = 2 "Protein_1"</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #molecules = 1</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #atoms_mol = 201</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> molblock (3):</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> moltype = 3 "Protein_2"</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #molecules = 1</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #atoms_mol = 231</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> molblock (4):</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> moltype = 4 "SOL"</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #molecules = 1398</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> #atoms_mol = 3</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
</div>
<div><br>
</div>
<div>#############</div>
<div><br>
</div>
<div>And here is the first 30 lines of the input .gro</div>
<div><br>
</div>
<div>RUN1</div>
<div><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">4652</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 1NA NA 1 1.111 1.195 1.100</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 2NA NA 2 0.903 0.086 0.133</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">...</span></div>
<div><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 25CL CL </span><a href="tel:25%C2%A0%C2%A0%202.684%C2%A0%C2%A0%202.864" value="+12526842864" target="_blank" style="color: rgb(17, 85, 204); font-family: arial, sans-serif; font-size: 13px; ">25
2.684 2.864</a><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 3.234</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 26CL CL </span><a href="tel:26%C2%A0%C2%A0%200.233%C2%A0%C2%A0%200.729" value="+12602330729" target="_blank" style="color: rgb(17, 85, 204); font-family: arial, sans-serif; font-size: 13px; ">26
0.233 0.729</a><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 2.132</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 27ACE CH3 27 3.073 2.376 1.686</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 27ACE HH31 28 3.163 2.414 1.665</span></div>
<div><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">...</span>
</div>
<div><br>
</div>
<div>
<div>###############################</div>
<div><br>
</div>
<div>And here is the first 30 lines of the output .gro after grompp and editconf -f .tpr</div>
<div><br>
</div>
<div>RUN1</div>
<div><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">4652</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 16NA NA 1 1.111 1.195 1.100</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 17NA NA 2 0.903 0.086 0.133</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">...</span> </div>
<div><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 40CL CL </span><a href="tel:25%C2%A0%C2%A0%202.684%C2%A0%C2%A0%202.864" value="+12526842864" target="_blank" style="color: rgb(17, 85, 204); font-family: arial, sans-serif; font-size: 13px; ">25
2.684 2.864</a><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 3.234</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 41CL CL </span><a href="tel:26%C2%A0%C2%A0%200.233%C2%A0%C2%A0%200.729" value="+12602330729" target="_blank" style="color: rgb(17, 85, 204); font-family: arial, sans-serif; font-size: 13px; ">26
0.233 0.729</a><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 2.132</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 1ACE CH3 27 3.073 2.376 1.686</span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">
<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "> 1ACE HH31 28 3.163 2.414 1.665</span></div>
<div><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; ">...</span>
</div>
<div><font color="#222222" face="arial, sans-serif" size="2"><br>
</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">########################</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2"><br>
</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">Finally, I tested this by creating an OPLS topology for either ALA or ACE-ALA. I then put two molecules</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">of the selected species in a box and ran grompp; editconf -f .tpr -o .gro and found that the atom numbers</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">started again back at zero only for the system containing ACE. This narrows it down to show that problem is</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">not system specific, nor does it depend on the presence of the NME residue.</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2"><br>
</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">Further, I tested with version 4.0.7 (pdb2gmx, grompp, editconf) and found that this problem did not exist.</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">Nevertheless, if I used version 4.5.5 of editconf to extract from the .tpr generated by 4.0.7 then I see improper</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">residue numbering.</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2"><br>
</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">It seems to me that there is some problem in the residue numbering routine that is used by editconf and trjconv</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">that exists at least in 4.5.3 and 4.5.5 but not in 4.0.7. This can be problematic for later analysis if, for example, a .ndx file is constructed from a .gro with non-sequential residue numbers. It
also seems to be leading to problems with our selections for genion.</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2"><br>
</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2">If anybody has encountered this and solved it, I'd love to hear about it.</font></div>
<div><font color="#222222" face="arial, sans-serif" size="2"><br>
</font></div>
</div>
<div>Thank you,</div>
<div>Chris.</div>
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