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

[Mark Abraham]

Sure, but by writing your model in .pdb you have thrown away important
information. If you can't write it in another format and won't re-solvate,
then you might have to try strategies like converting it to .gro with
editconf and fixing the numbering by hand/script.

Mark


On Wed, Aug 6, 2014 at 8:21 PM, WH <signoreguidami at 163.com> wrote:

> Thank you for your reply. I am just wondering is there anyway we can make
> pdb2gmx change the default digit number? I am doing a membrane protein, and
> I already have a ideal model as a pdb file. If I need to go over the
> solvate(or genbox in the 4.5.x version), by default waterbox setting the
> water will go into the lipid layer since the algorithm is just to put water
> into all the spaces, I may have to manually delete those water. If I can
> just transfer the model it will make life much easier and I can also
> compare with the known result. Thanks again for your time!
>
>
>
> >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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