[gmx-users] Protonate error

[David van der Spoel]

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This stuff is really outdated.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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se