<font face="georgia,serif">i tried to protonation of all ionizable residues in protein,<br>but it comes with an error.<br><br><br>Select group to process:<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>
Group 0 ( System) has 2443 elements<br>Group 1 ( Protein) has 2443 elements<br>Group 2 ( Protein-H) has 2443 elements<br>Group 3 ( C-alpha) has 299 elements<br>Group 4 ( Backbone) has 897 elements<br>
Group 5 ( MainChain) has 1197 elements<br>Group 6 (MainChain+Cb) has 1482 elements<br>Group 7 ( MainChain+H) has 1197 elements<br>Group 8 ( SideChain) has 1246 elements<br>Group 9 ( SideChain-H) has 1246 elements<br>
Select a group: 1<br>Selected 1: 'Protein'<br><br>Back Off! I just backed up prt_prot.pdb to ./#prt_prot.pdb.2#<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2.hdb<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2.atp<br>
Atomtype 1<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2-n.tdb<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx2-c.tdb<br>WARNING: atom CD not found in residue 10 while adding atom<br>
<br>-------------------------------------------------------<br>Program protonate_mpi_d, VERSION 4.0.5<br>Source code file: genhydro.c, line: 304<br><br>Fatal error:<br>Atom CD not found in residue ILE10 while adding hydrogens<br>
-------------------------------------------------------<br><br><br><br clear="all"></font><br>-- <br><b><span style="font-family: garamond,serif;">Best Regards,</span><br style="font-family: garamond,serif;"></b><br><span style="font-family: georgia,serif;">B. Sarath Kumar, M.S (By Research), </span><br style="font-family: georgia,serif;">
<span style="font-family: georgia,serif;">Centre for Biotechnology,</span><br style="font-family: georgia,serif;"><span style="font-family: georgia,serif;">Anna University, Chennai.</span><br><br><br>