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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Received on Sun Dec 12 2004 - 10:53:00 PST
