<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hello Everyone,<br>I have a same query, I asked before, but couldnt get a solution for that,<br>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.<br>I am pasting some part of end of my topology file's [atom] part here.<br><span style="font-weight: bold;"> 4883 CH1 493 LEU CG 2100 0 13.019 ; qtot -1.94</span><br style="font-weight: bold;"><span style="font-weight: bold;">
4884 CH3 493 LEU CD1 2100 0 15.035 ; qtot -1.94</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4885 CH3 493 LEU CD2 2100 0 15.035 ; qtot -1.94</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4886 C 493 LEU C 2101 0.38 12.011 ; qtot -1.56</span><br style="font-weight: bold;"><span style="font-weight:
bold;"> 4887 O 493 LEU O 2101 -0.38 15.9994 ; qtot -1.94</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4888 N 494 ARG N 2102 -0.28 14.0067 ; qtot -2.22</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4889 H 494 ARG H 2102 0.28 1.008 ; qtot -1.94</span><br style="font-weight: bold;"><span
style="font-weight: bold;"> 4890 CH1 494 ARG CA 2103 0 13.019 ; qtot -1.94</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4891 CH2 494 ARG CB 2103 0 14.027 ; qtot -1.94</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4892 CH2 494 ARG CG 2103 0 14.027 ; qtot -1.94</span><br
style="font-weight: bold;"><span style="font-weight: bold;"> 4893 CH2 494 ARG CD 2104 0.09 14.027 ; qtot -1.85</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4894 NE 494 ARG NE 2104 -0.11 14.0067 ; qtot -1.96</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4895 H 494 ARG HE 2104 0.24 1.008 ; qtot -1.72</span><br
style="font-weight: bold;"><span style="font-weight: bold;"> 4896 C 494 ARG CZ 2104 0.34 12.011 ; qtot -1.38</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4897 NZ 494 ARG NH1 2104 -0.26 14.0067 ; qtot -1.64</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4898 H 494 ARG HH11 2104 0.24 1.008 ; qtot -1.4</span><br style="font-weight:
bold;"><span style="font-weight: bold;"> 4899 H 494 ARG HH12 2104 0.24 1.008 ; qtot -1.16</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4900 NZ 494 ARG NH2 2104 -0.26 14.0067 ; qtot -1.42</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4901 H 494 ARG HH21 2104 0.24 1.008 ; qtot -1.18</span><br style="font-weight: bold;"><span
style="font-weight: bold;"> 4902 H 494 ARG HH22 2104 0.24 1.008 ; qtot -0.94</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4903 C 494 ARG C 2105 0.38 12.011 ; qtot -0.56</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4904 O 494 ARG O 2105 -0.38 15.9994 ; qtot -0.94</span><br style="font-weight: bold;"><span
style="font-weight: bold;"> 4905 N 495 LYSH N 2106 -0.28 14.0067 ; qtot -1.22</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4906 H 495 LYSH H 2106 0.28 1.008 ; qtot -0.94</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4907 CH1 495 LYSH CA 2107 0 13.019 ; qtot -0.94</span><br style="font-weight: bold;"><span
style="font-weight: bold;"> 4908 CH2 495 LYSH CB 2107 0 14.027 ; qtot -0.94</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4909 CH2 495 LYSH CG 2108 0 14.027 ; qtot -0.94</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4910 CH2 495 LYSH CD 2108 0 14.027 ; qtot -0.94</span><br style="font-weight:
bold;"><span style="font-weight: bold;"> 4911 CH2 495 LYSH CE 2109 0.127 14.027 ; qtot -0.813</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4912 NL 495 LYSH NZ 2109 0.129 14.0067 ; qtot -0.684</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4913 H 495 LYSH HZ1 2109 0.248 1.008 ; qtot -0.436</span><br style="font-weight: bold;"><span style="font-weight:
bold;"> 4914 H 495 LYSH HZ2 2109 0.248 1.008 ; qtot -0.188</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4915 H 495 LYSH HZ3 2109 0.248 1.008 ; qtot 0.06</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4916 C 495 LYSH C 2110 0.27 12.011 ; qtot 0.33</span><br style="font-weight: bold;"><span style="font-weight: bold;">
4917 OM 495 LYSH O1 2110 -0.635 15.9994 ; qtot -0.305</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4918 OM 495 LYSH O2 2110 -0.635 15.9994 ; qtot -0.94</span><br style="font-weight: bold;"><span style="font-weight: bold;"> 4919 MG2+ 496 MG MG 2111 2 24.305 ; qtot 1.06</span><br><br>there are so many non-integral charges here for residues,<br>please help.<br>Thanks and regards
<br><br><div>--<br>Sonali Dhindwal</div></td></tr></table><br>Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php