VMD-L Mailing List

From: Do Yong Kim (kdy2002_at_gmail.com)
Date: Tue Oct 01 2013 - 10:59:08 CDT

Hello all,

I have made a custom residue that has amidated C-terminus and when I apply
ribbon or cartoon representation, the representation ends at the residue
before the modified C-terminus.

I looked at the naming of atoms and I cannot figure out what is wrong.

any help will be greatly appreciated.

ATOM 151 N GLY 9 17.077 3.182 -1.481 -0.4157 1.5500
ATOM 152 H GLY 9 17.659 2.326 -1.475 0.2719 1.3000
ATOM 153 CA GLY 9 17.538 4.210 -0.519 -0.0252 1.7000
ATOM 154 HA2 GLY 9 16.911 5.034 -0.690 0.0698 1.3000
ATOM 155 HA3 GLY 9 17.467 3.835 0.464 0.0698 1.3000
ATOM 156 C GLY 9 18.984 4.574 -0.813 0.5973 1.7000
ATOM 157 O GLY 9 19.857 4.285 -0.045 -0.5679 1.5000
ATOM 158 N LEU 10 19.176 5.285 -1.921 -0.4157 1.5500
ATOM 159 H LEU 10 18.329 5.472 -2.461 0.2719 1.3000
ATOM 160 CA LEU 10 20.479 5.762 -2.425 -0.0518 1.7000
ATOM 161 HA LEU 10 21.198 4.984 -2.238 0.0922 1.3000
ATOM 162 CB LEU 10 20.272 5.969 -3.914 -0.1102 1.7000
ATOM 163 HB2 LEU 10 19.663 5.159 -4.332 0.0457 1.3000
ATOM 164 HB3 LEU 10 19.647 6.821 -4.027 0.0457 1.3000
ATOM 165 CG LEU 10 21.491 6.172 -4.886 0.3531 1.7000
ATOM 166 HG LEU 10 22.167 6.981 -4.628 -0.0361 1.3000
ATOM 167 CD1 LEU 10 22.313 4.826 -4.947 -0.4121 1.7000
ATOM 168 1HD1 LEU 10 21.797 4.077 -5.554 0.1000 1.3000
ATOM 169 2HD1 LEU 10 23.264 5.012 -5.534 0.1000 1.3000
ATOM 170 3HD1 LEU 10 22.591 4.441 -3.951 0.1000 1.3000
ATOM 171 CD2 LEU 10 21.017 6.580 -6.304 -0.4121 1.7000
ATOM 172 1HD2 LEU 10 21.857 6.842 -6.923 0.1000 1.3000
ATOM 173 2HD2 LEU 10 20.539 5.695 -6.776 0.1000 1.3000
ATOM 174 3HD2 LEU 10 20.362 7.480 -6.158 0.1000 1.3000
ATOM 175 C LEU 10 20.983 7.004 -1.667 0.5973 1.7000
ATOM 176 O LEU 10 21.409 7.952 -2.301 -0.5679 1.5000
ATOM 197 N MET 11 20.897 7.069 -0.284 -0.5006 1.5500
ATOM 178 H MET 11 20.444 6.319 0.125 0.3432 1.3000
ATOM 179 CA MET 11 21.328 8.073 0.457 0.2845 1.7000
ATOM 180 HA MET 11 22.014 8.644 -0.164 0.0404 1.3000
ATOM 181 CB MET 11 20.141 9.033 0.646 -0.0168 1.7000
ATOM 182 HB2 MET 11 19.955 9.272 -0.344 0.0517 1.3000
ATOM 183 HB3 MET 11 19.343 8.513 1.131 0.0517 1.3000
ATOM 184 CG MET 11 20.371 10.394 1.376 -0.1338 1.7000
ATOM 185 HG2 MET 11 20.178 10.409 2.424 0.0936 1.3000
ATOM 186 HG3 MET 11 21.430 10.620 1.195 0.0936 1.3000
ATOM 187 SD MET 11 19.463 11.757 0.838 -0.2641 1.8000
ATOM 188 CE MET 11 19.667 11.609 -0.938 -0.1162 1.7000
ATOM 189 HE1 MET 11 20.643 11.257 -1.066 0.0842 1.3000
ATOM 190 HE2 MET 11 19.021 10.777 -1.371 0.0842 1.3000
ATOM 191 HE3 MET 11 19.393 12.561 -1.311 0.0842 1.3000
ATOM 192 NE MET 11 21.838 7.604 1.609 -0.8113 1.5500
ATOM 193 1HE1 MET 11 21.817 6.649 1.826 0.3432 1.3000
ATOM 194 1HE2 MET 11 22.341 8.182 2.225 0.3432 1.3000