[gmx-users] pdb2gmx cannot generate the right residue and atom numbers
mark.j.abraham at gmail.com
Thu Aug 7 07:19:55 CEST 2014
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.
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
> >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
> >> .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
> >> 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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