[gmx-users] pdb2gmx cannot generate the right residue and atom numbers
mark.j.abraham at gmail.com
Tue Aug 5 16:33:33 CEST 2014
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.
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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