[gmx-users] Protonate error

[Sarath Kumar]

i tried to protonation of all ionizable residues in protein,
but it comes with an error.


Select group to process:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group     0 (      System) has  2443 elements
Group     1 (     Protein) has  2443 elements
Group     2 (   Protein-H) has  2443 elements
Group     3 (     C-alpha) has   299 elements
Group     4 (    Backbone) has   897 elements
Group     5 (   MainChain) has  1197 elements
Group     6 (MainChain+Cb) has  1482 elements
Group     7 ( MainChain+H) has  1197 elements
Group     8 (   SideChain) has  1246 elements
Group     9 ( SideChain-H) has  1246 elements
Select a group: 1
Selected 1: 'Protein'

Back Off! I just backed up prt_prot.pdb to ./#prt_prot.pdb.2#
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2.hdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2.atp
Atomtype 1
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2-n.tdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2-c.tdb
WARNING: atom CD not found in residue 10 while adding atom

-------------------------------------------------------
Program protonate_mpi_d, VERSION 4.0.5
Source code file: genhydro.c, line: 304

Fatal error:
Atom CD not found in residue ILE10 while adding hydrogens
-------------------------------------------------------




-- 
*Best Regards,
*
B. Sarath Kumar, M.S (By Research),
Centre for Biotechnology,
Anna University, Chennai.
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