[gmx-users] The output .Gro cannot be generated

Panichakorn Jaiyong nuch_nicha at yahoo.com
Tue Aug 14 14:19:43 CEST 2007


My molecule is the cycloheptapeptide which contains a proline ring. The first  problem is the disapperance of 7 hydrogen atoms in rtp file, so I run pdb2gmx with -ignh to ignore them and using Gromacs force field. The second one is the warning that atom CA not found in residue 8 while adding atom.

How does to solve with this?
  I try to pose the pdb in Prodrg site for a request of the .top file, but anything turns to me for 3 weeks.
It appears after select a forcefield like this:

Opening library file /usr/share/gromacs/top/ffgmx.rtp
Opening library file /usr/share/gromacs/top/aminoacids.dat
Reading TrialcordyhepA.pdb...
', 64 atomshepA
Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 22 residues with 64 atoms

  chain  #res #atoms
  1 ' '    22     64

All occupancies are one
Opening library file /usr/share/gromacs/top/ffgmx.atp
Atomtype 54
Reading residue database... (ffgmx)
Opening library file /usr/share/gromacs/top/ffgmx.rtp
Residue 98
Sorting it all out...
Opening library file /usr/share/gromacs/top/ffgmx.hdb
Opening library file /usr/share/gromacs/top/ffgmx-n.tdb
Opening library file /usr/share/gromacs/top/ffgmx-c.tdb
Processing chain 1 (64 atoms, 22 residues)
There are 7 donors and 8 acceptors
There are 12 hydrogen bonds
Checking for duplicate atoms....
Now there are 23 atoms. Deleted 41 duplicates.
Opening library file /usr/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
N-terminus: NH3+
C-terminus: COO-
WARNING: atom CA not found in residue 8 while adding atom
Program pdb2gmx, VERSION 3.3
Source code file: genhydro.c, line: 304

Fatal error:
Atom CA not found in residue Tyr8 while adding hydrogens

Thank you in advance,

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