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

[lina]

On Wed, Aug 3, 2011 at 9:13 PM, maria goranovic
<mariagoranovic at gmail.com> 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?
> 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
>
>

There is a problem in your in.gro.

try:

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
    2SOL     OW    6  12.025   1.421  -1.203
    2SOL    HW1    7  12.125   1.421  -1.203
    2SOL    HW2    8  11.993   1.516  -1.203
20 20 20

then there will be no problem.

>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
> --
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-- 
Best Regards,

lina