Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb

From: <sunita.tifrh.res.in>
Date: Wed, 10 Sep 2014 14:17:21 +0530

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 - 02:00:02 PDT
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