[gmx-users] bug in editconf for making a box ? combined two residues into one

[maria goranovic]

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?

Interestingly, grompp does not complain that the residue PHO has 8 atoms
instead of 5 as in the topology file.

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
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