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input PDB contains hydrogens but not named H ? #9

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HWaymentSteele opened this issue Mar 27, 2024 · 0 comments
Open

input PDB contains hydrogens but not named H ? #9

HWaymentSteele opened this issue Mar 27, 2024 · 0 comments

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@HWaymentSteele
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Hi! I'm trying to use with an input pdb formatted like this:

ATOM      1  N   GLY     1     -11.586  12.453  18.203  1.00  0.00           N
ATOM      2  CA  GLY     1     -11.312  12.859  16.828  1.00  0.00           C
ATOM      3  C   GLY     1     -11.195  11.688  15.875  1.00  0.00           C
ATOM      4  O   GLY     1     -10.867  10.578  16.281  1.00  0.00           O
ATOM      5  HA1 GLY     1     -12.096  13.529  16.475  1.00  0.00           H
ATOM      6  HA2 GLY     1     -10.348  13.364  16.774  1.00  0.00           H
ATOM      7  HT1 GLY     1     -11.662  13.305  18.793  1.00  0.00           H
ATOM      8  HT2 GLY     1     -10.810  11.855  18.553  1.00  0.00           H
ATOM      9  HT3 GLY     1     -12.479  11.924  18.246  1.00  0.00           H
ATOM     10  N   ALA     2     -12.281  11.211  15.289  1.00  0.00           N

I get a warning that no hydrogens are detected and performance will be bad if I leave the atom name in field 3 as is -- HA1, HA2, etc. I could figure out how to convert, but is the performance actually being impacted if it's not recognizing these hydrogen atom names? Thanks so much!

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