AMBER Archive (2006)

Subject: AMBER: Leap: neutralising the charge

From: Miguel Ferreira (tetrass_at_hotmail.com)
Date: Tue Jun 27 2006 - 04:49:36 CDT

Dear amber users,

I have several complexes protein-ligand (protein is the same in all of
them), with a total charge of -1. For some of them leap assign the correct
charge and hence, is able to neutralize the total charge, but for others,
leap says the charge is -0,9995 or -0,9997.
For instance:

>$AMBERHOME/exe/tleap -s -f leaprc.ff99
> source leaprc.gaff
> mods = loadamberparams ligand5.frcmod
> loadoff ligand5.off
> tudo = loadpdb complex5.pdb
Loading PDB file: ./complex5.pdb
total atoms in file: 1924
Leap added 1952 missing atoms according to residue templates:
1952 H / lone pairs
>addions tudo Na+ 0
0.999700 0 1 0
0 Na+ ion required to neutralize.
Adding 0 counter ions to "tudo" using 1A grid

What I did was to modify the mol2 file, subtracting -0.0003 to the charge of
a very electropositive atom (charge ~1.4). Is this normal and what I did to
solve is correct?

Thanks in advance
Miguel

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