Hi,
One simple way you can check if the number of waters etc is indeed
different between the Amber parm file and the PDB is to load each into
cpptraj and compare output from the 'parminfo' command, e.g.
$ ~/Amber/amber14/bin/cpptraj tz2.truncoct.parm7
CPPTRAJ: Trajectory Analysis. V14.05
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
Reading 'tz2.truncoct.parm7' as Amber Topology
> parminfo
Topology tz2.truncoct.parm7 contains 5827 atoms.
1882 residues.
1870 molecules.
5834 bonds (5711 to H, 123 other).
402 angles (233 with H, 169 other).
853 dihedrals (481 with H, 372 other).
Box: Trunc. Oct.
1869 solvent molecules.
Final solute residue is 13
GB radii set: modified Bondi radii (mbondi)
>
-Dan
On Mon, Sep 8, 2014 at 8:17 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Sep 08 2014 - 08:30:04 PDT
