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 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 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.
Thanks and regards
--
Sonali Dhindwal
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