[gmx-users] non-integral charge on my modeled protein structure

[Mark Abraham]

On 10/04/2010 4:08 PM, sonali dhindwal wrote:
> Hello Everyone,
> I have a same query, I asked before, but couldnt get a solution for that,
> I have one modelled protein strucutre,,and when I run pdb2gmx to
> generate topolgy file, it gives charge in non-integral value. In

Then something is broken. Are your termini sane? What's that Mg doing?

> terminal then it gives warning of protein having non-integral charge.
> Moreover, in the toplogy file qtot for the last residue comes out to be
> different than that is shown in terminal as warning.

I don't believe you are looking at a .top file that corresponds to the 
terminal output.

> I am pasting some part of end of my topology file's [atom] part here.
> 4883 CH1 493 LEU CG 2100 0 13.019 ; qtot -1.94
> 4884 CH3 493 LEU CD1 2100 0 15.035 ; qtot -1.94
> 4885 CH3 493 LEU CD2 2100 0 15.035 ; qtot -1.94
> 4886 C 493 LEU C 2101 0.38 12.011 ; qtot -1.56
> 4887 O 493 LEU O 2101 -0.38 15.9994 ; qtot -1.94
> 4888 N 494 ARG N 2102 -0.28 14.0067 ; qtot -2.22
> 4889 H 494 ARG H 2102 0.28 1.008 ; qtot -1.94
> 4890 CH1 494 ARG CA 2103 0 13.019 ; qtot -1.94
> 4891 CH2 494 ARG CB 2103 0 14.027 ; qtot -1.94
> 4892 CH2 494 ARG CG 2103 0 14.027 ; qtot -1.94
> 4893 CH2 494 ARG CD 2104 0.09 14.027 ; qtot -1.85
> 4894 NE 494 ARG NE 2104 -0.11 14.0067 ; qtot -1.96
> 4895 H 494 ARG HE 2104 0.24 1.008 ; qtot -1.72
> 4896 C 494 ARG CZ 2104 0.34 12.011 ; qtot -1.38
> 4897 NZ 494 ARG NH1 2104 -0.26 14.0067 ; qtot -1.64
> 4898 H 494 ARG HH11 2104 0.24 1.008 ; qtot -1.4
> 4899 H 494 ARG HH12 2104 0.24 1.008 ; qtot -1.16
> 4900 NZ 494 ARG NH2 2104 -0.26 14.0067 ; qtot -1.42
> 4901 H 494 ARG HH21 2104 0.24 1.008 ; qtot -1.18
> 4902 H 494 ARG HH22 2104 0.24 1.008 ; qtot -0.94
> 4903 C 494 ARG C 2105 0.38 12.011 ; qtot -0.56
> 4904 O 494 ARG O 2105 -0.38 15.9994 ; qtot -0.94
> 4905 N 495 LYSH N 2106 -0.28 14.0067 ; qtot -1.22
> 4906 H 495 LYSH H 2106 0.28 1.008 ; qtot -0.94
> 4907 CH1 495 LYSH CA 2107 0 13.019 ; qtot -0.94
> 4908 CH2 495 LYSH CB 2107 0 14.027 ; qtot -0.94
> 4909 CH2 495 LYSH CG 2108 0 14.027 ; qtot -0.94
> 4910 CH2 495 LYSH CD 2108 0 14.027 ; qtot -0.94
> 4911 CH2 495 LYSH CE 2109 0.127 14.027 ; qtot -0.813
> 4912 NL 495 LYSH NZ 2109 0.129 14.0067 ; qtot -0.684
> 4913 H 495 LYSH HZ1 2109 0.248 1.008 ; qtot -0.436
> 4914 H 495 LYSH HZ2 2109 0.248 1.008 ; qtot -0.188
> 4915 H 495 LYSH HZ3 2109 0.248 1.008 ; qtot 0.06
> 4916 C 495 LYSH C 2110 0.27 12.011 ; qtot 0.33
> 4917 OM 495 LYSH O1 2110 -0.635 15.9994 ; qtot -0.305
> 4918 OM 495 LYSH O2 2110 -0.635 15.9994 ; qtot -0.94
> 4919 MG2+ 496 MG MG 2111 2 24.305 ; qtot 1.06
>
> there are so many non-integral charges here for residues,
> please help.

No, the residues here have integral charges. The partial sum over all 
residues is non-integral. Go and find the first-non-integral one and fix it.

Mark