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

[João Martins]

Is there a specific reason why you're not adding the water using genbox and
genion? If that's not the case you can simply delete the waters from the
pdb and only convert the rest of the system. Then you can solvate, set your
box boundaries and add ions.

Best,
João



 *Joao Martins*

joaomartins139 at gmail.com


On Tue, Aug 5, 2014 at 6:09 AM, 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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