[gmx-users] pdb2gmx cannot generate the right residue and atom numbers

[Mark Abraham]

In addition to what Joao said, the fixed-width .pdb format is fundamentally
unsuited to large systems. You need to find a way to avoid using such a
.pdb file as input to pdb2gmx; either solvate later, or use a different
format for input.

Mark


On Mon, Aug 4, 2014 at 11:09 PM, WH <signoreguidami at 163.com> wrote:

> Dear Gromacs users,
>
> I want to use Gromacs to process a system with more than 80000 water
> moelcules. However, when use pdb2gmx to deal the the pdb file, the out put
> .gro file has the form like this:
>  3409HOH    HW234995  -5.617  -6.883  -8.771
>  3409HOH     OW34996  -6.108  -6.959  -7.760
>  3409HOH    HW134997  -6.107  -6.973  -7.855
>  3409HOH    HW234998  -6.199  -6.971  -7.735
>  3409HOH     OW34999  -4.964  -8.455  -9.110
>  3409HOH    HW135000  -5.054  -8.441  -9.081
>  3409HOH    HW235001  -4.939  -8.372  -9.150
>  3409HOH     OW35002  -6.157  -7.576  -8.913
>  3409HOH    HW135003  -6.187  -7.499  -8.962
>
> Only 4 digits will be used for the residue number and 5 for the atom
> number. Thus, the actual residue number and atom number cannot be written
> correctly and lead to failure for the MD simulation.
> Does anyone know how to fix this problem? I really appreciate it.
> --
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