On Wed, Aug 3, 2011 at 9:13 PM, maria goranovic
<mariagorano...@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
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