Looks like the problem exists when the number of water molecules exceed
more than 9999. Please try to find out why is so?
With regards,
Sunita
> Hi Dac,
>
> There is problem when pdb file is created using "ambpdb" command. The ATOM
> numbers are correct but Water residues (WAT) are not numbered correctly.
> In the test.pdb file after resid 9999, residue numbering starts again with
> 0, 1, 2......3216. This number does not match with topology file. When I
> tried with other PDB file it shows the same thing. That is after resid
> 9999, renumbering starts again.
>
> There is absolutely no problem with "savepdb". It matches with topology
> file.
>
> Please try with the attached PDB file. First generate the .prmtop and
> incrp and try to convert it using ambpdb. I tried with 2 - 3 different
> protein PDB files. I got similar problem. I tried with a short peptide and
> surprisingly there was no problem with that.
>
>
> Thank you.
> Sunita
>
>
>
>
>> On Mon, Sep 08, 2014, sunita.tifrh.res.in wrote:
>>> Why there is mismatch in the number of atoms when created using
> "ambpdb"
>>> and "savepdb" as follow? ambpdb gives more number of water molecules.
> The pdb file created using "savepdb" gives correct number of atoms in
> the
>>> system.
>>> =====================
>>> source leaprc.ff99SB
>>> m = loadpdb minimized_structure.pdb
>>> addions m Cl- 0
>>> solvatebox m TIP3PBOX 14
>>> saveamberparm m UVI_control_solion.prmtop UVI_control_solion.inpcrd
> savepdb m UVI_solion.pdb
>>> quit
>>> ======================
>>> ambpdb -p UVI_control_solion.prmtop < UVI_control_solion.inpcrd >
>>> test.pdb
>>> ======================
>> This should not happen, and I have never seen it. Can you be more
>> specific
>> about what you mean by "more number of water molecules"? Does the
> number
>> of
>> atoms in test.pdb match the numbers at the top of the prmtop and inpcrd
> file?
>> Same question for UVI_solion.pdb. (To find the number of atoms, use a
> command
>> like "grep ATOM test.pdb | wc"). It might give a clue if you told us
> the
>> exact number of atoms in each of the four files.
>> ...dac
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Received on Wed Sep 10 2014 - 02:30:02 PDT
