[gmx-users] bug in editconf for making a box ? combined two residues into one
mariagoranovic at gmail.com
Wed Aug 3 15:51:18 CEST 2011
Thanks for the replies. I guess it is a very small bug. However, here is
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
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
Thank you for helping,
On Wed, Aug 3, 2011 at 3:38 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> maria goranovic wrote:
>> 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.
> 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
>> 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
>> 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
> 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
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Technical University of Denmark
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