AMBER Archive (2004)

Subject: Re: AMBER: Why the charge is not an integer?

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Sun Dec 12 2004 - 10:21:32 CST

Hi,

It's possibly round-off error. I assume you developed charges for the
neutral residues. If the net charge of each residue is slightly off
integer and you have plenty of such residues in your protein, then it's
possible the sum is off even more.

Regards,

Guanglei

mmv wrote:
> Hi all,
> I want to run a MD simulation under acidic pH,so I change HIS/ASP/GLU to
> HIP/AS4/GL4 in the pdb file,respectively.Then I run tleap as following:
>
>
>>source leaprc.ff99
>
> ----- Source: /usr/local/amber8/dat/leap/cmd/leaprc.ff99
> ----- Source of /usr/local/amber8/dat/leap/cmd/leaprc.ff99 done
> Log file: ./leap.log
> Loading parameters: /usr/local/amber8/dat/leap/parm/parm99.dat
> Loading library: /usr/local/amber8/dat/leap/lib/all_nucleic94.lib
> Loading library: /usr/local/amber8/dat/leap/lib/all_amino94.lib
> Loading library: /usr/local/amber8/dat/leap/lib/all_aminoct94.lib
> Loading library: /usr/local/amber8/dat/leap/lib/all_aminont94.lib
> Loading library: /usr/local/amber8/dat/leap/lib/ions94.lib
> Loading library: /usr/local/amber8/dat/leap/lib/solvents.lib
>
>>loadAmberParams frcmod.mod_phipsi.1
>
> Loading parameters: /usr/local/amber8/dat/leap/parm/frcmod.mod_phipsi.1
> Reading force field mod type file (frcmod)
>
>>set default PBRadii mbondi2
>
> Using H(N)-modified Bondi radii
>
>>loadoff constph.lib
>
> Loading library: /usr/local/amber8/dat/leap/lib/constph.lib
>
>>loadamberparams frcmod.constph
>
> Loading parameters: /usr/local/amber8/dat/leap/parm/frcmod.constph
> Reading force field mod type file (frcmod)
>
>>model = loadpdb "model.model.pdb"
>
> Loading PDB file: ./model.model.pdb
> total atoms in file: 1109
> Leap added 1108 missing atoms according to residue templates:
> 1108 H / lone pairs
>
>>solvatebox model TIP3PBOX 10.0
>
> Solute vdw bounding box: 49.800 49.236 36.162
> Total bounding box for atom centers: 69.800 69.236 56.162
> Solvent unit box: 18.774 18.774 18.774
> Total vdw box size: 72.559 71.808 58.910 angstroms.
> Volume: 306943.555 A^3
> Total mass 148428.024 amu, Density 0.803 g/cc
> Added 7355 residues.
>
>>charge model
>
> Total unperturbed charge: 6.9985
> Total perturbed charge: 6.9985
>
> Here comes the problem ,the charge of my molecular is not an integer.
> So when I try to add Cl- ions to neutralize the system,only 6 ions are
> added.Thus the net charge is 0.9985.
>
> Where does the fractional charge come from?And how can I neutralize the
> system?
>
> Thanks!
> Shuli Kang
>
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