it's probably not the names themselves, but the columns the names use in the
file. does leap say anything about having extra atoms?
On Tue, May 19, 2009 at 12:20 PM, Mark M Huntress <markmh.bgsu.edu> wrote:
> Hi, I have a pdb that was saved on VMD, and AMBER doesn't want to load it
> right.
>
> It creates about 400 new hydrogens, because it apparently cannot recognize
> the hydrogens that are already there.
>
> For example, these are some of the H's it adds when I do "mol = loadpdb
> file.pdb" :
> Created a new atom named: 2HB within residue: .R<ARG 136>
> Created a new atom named: 3HB within residue: .R<ARG 136>
> Created a new atom named: 2HG within residue: .R<ARG 136>
> Created a new atom named: 3HG within residue: .R<ARG 136>
> Created a new atom named: 2HD within residue: .R<ARG 136>
> Created a new atom named: 3HD within residue: .R<ARG 136>
>
> but these atoms are already in the pdb file:
>
> ATOM 2146 N ARG A 136 -15.329 -2.598 -9.210 1.00 0.00
> ATOM 2147 H ARG A 136 -15.332 -3.533 -9.614 1.00 0.00
> ATOM 2148 CA ARG A 136 -15.497 -1.426 -10.034 1.00 0.00
> ATOM 2149 HA ARG A 136 -14.896 -0.566 -9.736 1.00 0.00
> ATOM 2150 CB ARG A 136 -15.344 -1.704 -11.501 1.00 0.00
> ATOM 2151 2HB ARG A 136 -15.675 -2.780 -11.830 1.00 0.00
> ATOM 2152 3HB ARG A 136 -15.854 -0.894 -12.075 1.00 0.00
> ATOM 2153 CG ARG A 136 -13.870 -1.699 -11.959 1.00 0.00
> ATOM 2154 2HG ARG A 136 -13.437 -0.753 -11.777 1.00 0.00
> ATOM 2155 3HG ARG A 136 -13.283 -2.423 -11.422 1.00 0.00
> ATOM 2156 CD ARG A 136 -13.865 -2.007 -13.406 1.00 0.00
> ATOM 2157 2HD ARG A 136 -14.316 -2.963 -13.526 1.00 0.00
> ATOM 2158 3HD ARG A 136 -14.529 -1.226 -13.934 1.00 0.00
> ATOM 2159 NE ARG A 136 -12.541 -1.883 -14.120 1.00 0.00
> ATOM 2160 HE ARG A 136 -12.134 -0.944 -14.162 1.00 0.00
> ATOM 2161 CZ ARG A 136 -11.668 -2.878 -14.399 1.00 0.00
> ATOM 2162 NH1 ARG A 136 -11.836 -4.163 -14.169 1.00 0.00
> ATOM 2163 1HH1 ARG A 136 -12.614 -4.424 -13.626 1.00 0.00
> ATOM 2164 2HH1 ARG A 136 -11.124 -4.965 -14.312 1.00 0.00
> ATOM 2165 NH2 ARG A 136 -10.626 -2.634 -15.083 1.00 0.00
> ATOM 2166 1HH2 ARG A 136 -10.436 -1.665 -15.341 1.00 0.00
> ATOM 2167 2HH2 ARG A 136 -10.050 -3.400 -15.471 1.00 0.00
> ATOM 2168 C ARG A 136 -16.923 -0.961 -9.830 1.00 0.00
> ATOM 2169 O ARG A 136 -17.896 -1.685 -9.808 1.00 0.00
>
>
> Is this maybe a problem with atom order? Is there something simple that I
> am missing?
>
> Thanks,
> Mark
>
>
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Received on Wed May 20 2009 - 17:30:50 PDT
