On 2010-08-14 11.36, Sarath Kumar wrote:
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
-------------------------------------------------------
This stuff is really outdated. Maybe it helps to rename the CD1 atoms to
CD in your pdb file.
--
*Best Regards,
*
B. Sarath Kumar, M.S (By Research),
Centre for Biotechnology,
Anna University, Chennai.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
--
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