[gmx-users] request

[Dinesh Pinisetty]

Hi all,
         I have known about GROMACS last month by this you can make out how
new I am in this field.I have many questions to ask but first let me ask
one in this mail.
         I started with the sample MD code given in
md.chem.rug.nl/education/mdcourse2004,its on lysozymes.The pdb file was
imported from PDB data base in this tutorial the pdb file imported was
1AKI.pdb,when I ran the code importing this as given in this site code was
running but when I changed the pdb file i.e when I import 1IWZ.pdb and try
to run the simulation I was getting an error in the first step itself i.e
when I was trying to create a topology and gromacs files.
error was as follows

FATAL error: Atom HA in residue LYSH1 not found in rtp entry  with 13 atoms
while sorting atoms.Maybe different protonation state.Remove this hydrogen
or choose a different protonation state.Option -ignh will ignore all
hydrogens in the input.

When I tried to import another pdb file for DMPC 1SMZ.pdb and try to create
.top and .gro files I was getting the following error.

FATAL error: Atom HA1 in residue GLY1 not found in rtp entry  with 5 atoms
while sorting atoms.Maybe different protonation state.Remove this hydrogen
or choose a different protonation state.Option -ignh will ignore all
hydrogens in the input.

When I tried import another pdb file for GLYCEROL I was getting the
following error

FATAL error:Atom A01 in residue NDPH1 not found in rtp entry with 56 atoms
while sorting atoms.

Please bear with me for typing such a long mail,I just want  to be clear in
mentioning the errors to you all as I am a beginner I do not even know
whether these errors are simple .I am sorry if I am disturbing you by
typing such a silly mail if this mail not worthy.
 Please someone help me out in this regard,I hope someone of you will bear
me and do the needful.
         Thanks a lot in advance for all of you.

Thanking you,
Yours sincerely,
Dinesh.