Thanks for the replies. I guess it is a very small bug. However, here is another:<div><br></div><div>I have a 2-protein complex in water. The first protein residues numbers are from residues 4 to 14, and the other from 5 to 9. In the INPUT .gro file to grompp, I have a continuous numbering of residues from 4 to 19 (4 to 14+5). However, after an energy minimization, gromacs writes out a .gro file which preserves the original numbering (4 to 14 and 5 to 9) instead of a numbering from 4 to 19. Why does it do that? I can see the problem with such a numbering because I can never unambiguously select "residue number 6" if I want to make an index file. How does one go about fixing this? </div>
<div><br></div><div>I made the original input .gro file by using : editconf -f in.gro -o out.gro -resnr 4</div><div><br></div><div>In the topology file, I read in protein_A.itp and protein_B.itp which start from the original pdb residue number (4 and 5 respectively for the two chains)</div>
<div><br></div><div>Thank you for helping,</div><div><br></div><div>Maria</div><div><br></div><div><br></div><div><br><div class="gmail_quote">On Wed, Aug 3, 2011 at 3:38 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi<br>
<br>
I am using editconf to set my box to the right size using:<br>
<br>
editconf -f in.gro -o out.gro -box 30 30 30<br>
<br>
gromacs v. 4.5.3<br>
<br>
For this example, my system contains a phosphate anion and a water molecule. After editconf runs, it changes the residue name SOL of the water molecule to the residue name PHO for phosphate, because both have the same residue number (1). Is this not a bug, or am I doing something really silly? One can always try to run a simulation of an amino acid in water, and the error below would be replicated? <br>
</blockquote>
<br></div>
I suspect so. You can file a bug report, but it will probably remain a very low priority for now. One normally does not number a coordinate file this way. Each residue should be numbered independently.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Interestingly, grompp does not complain that the residue PHO has 8 atoms instead of 5 as in the topology file.<br>
<br>
</blockquote>
<br></div>
AFAIK grompp only pays attention to atom names, which in this case likely match the topology without an issue.<br>
<br>
-Justin<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I do not see this problem if the residue number of the water molecule is 2 instead of 1.<br>
<br>
Below are the two .gro files, before and after running the above command.<br>
<br>
<br>
GROtesk MACabre and Sinister<br>
8<br>
1PHO O1P 1 13.422 2.753 5.900<br>
1PHO P <a href="tel:2%20%2013.250%20%20%202.818" value="+12132502818" target="_blank">2 13.250 2.818</a> 5.976<br>
1PHO O2P 3 13.193 2.967 5.853<br>
1PHO O3P <a href="tel:4%20%2013.263%20%20%202.864" value="+14132632864" target="_blank">4 13.263 2.864</a> 6.169<br>
1PHO O4P 5 13.118 2.672 5.939<br>
1SOL OW 1 12.025 1.421 -1.203<br>
1SOL HW1 2 12.125 1.421 -1.203<br>
1SOL HW2 3 11.993 1.516 -1.203<br>
20 20 20<br>
<br>
<br>
GROtesk MACabre and Sinister<br>
8<br>
1PHO O1P 1 15.623 15.449 17.622<br>
1PHO P 2 15.451 15.514 17.697<br>
1PHO O2P 3 15.394 15.663 17.574<br>
1PHO O3P 4 15.464 15.560 17.890<br>
1PHO O4P 5 15.319 15.368 17.660<br>
1PHO OW 6 14.226 14.117 10.518<br>
1PHO HW1 7 14.326 14.117 10.518<br>
1PHO HW2 8 14.194 14.212 10.518<br>
30.00000 30.00000 30.00000<br>
<br>
<br>
<br>
<br>
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<br>
</blockquote>
<br></div></div>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
-- <br></font><div><div></div><div class="h5">
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>
</div>