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

WH signoreguidami at 163.com
Thu Aug 7 03:22:06 CEST 2014

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.
>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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