Thanks for the replies. I guess it is a very small bug. However, here is another:
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? I made the original input .gro file by using : editconf -f in.gro -o out.gro -resnr 4 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) Thank you for helping, Maria On Wed, Aug 3, 2011 at 3:38 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > maria goranovic wrote: > >> Hi >> >> I am using editconf to set my box to the right size using: >> >> editconf -f in.gro -o out.gro -box 30 30 30 >> >> gromacs v. 4.5.3 >> >> 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? >> > > 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. > > > Interestingly, grompp does not complain that the residue PHO has 8 atoms >> instead of 5 as in the topology file. >> >> > AFAIK grompp only pays attention to atom names, which in this case likely > match the topology without an issue. > > -Justin > > > I do not see this problem if the residue number of the water molecule is 2 >> instead of 1. >> >> Below are the two .gro files, before and after running the above command. >> >> >> GROtesk MACabre and Sinister >> 8 >> 1PHO O1P 1 13.422 2.753 5.900 >> 1PHO P 2 13.250 2.818 5.976 >> 1PHO O2P 3 13.193 2.967 5.853 >> 1PHO O3P 4 13.263 2.864 6.169 >> 1PHO O4P 5 13.118 2.672 5.939 >> 1SOL OW 1 12.025 1.421 -1.203 >> 1SOL HW1 2 12.125 1.421 -1.203 >> 1SOL HW2 3 11.993 1.516 -1.203 >> 20 20 20 >> >> >> GROtesk MACabre and Sinister >> 8 >> 1PHO O1P 1 15.623 15.449 17.622 >> 1PHO P 2 15.451 15.514 17.697 >> 1PHO O2P 3 15.394 15.663 17.574 >> 1PHO O3P 4 15.464 15.560 17.890 >> 1PHO O4P 5 15.319 15.368 17.660 >> 1PHO OW 6 14.226 14.117 10.518 >> 1PHO HW1 7 14.326 14.117 10.518 >> 1PHO HW2 8 14.194 14.212 10.518 >> 30.00000 30.00000 30.00000 >> >> >> >> >> >> -- >> Maria G. >> Technical University of Denmark >> Copenhagen >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Maria G. Technical University of Denmark Copenhagen
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