[gmx-users] request

[Oliver Lange]

Hi Dinesh,

you should use the option -ignh, when you import pdb files with pdb2gmx.
This options means that the hydrogens, named in a gromacs-unfriendly-way, are ignored. 
pdb2gmx places hydrogens by itself, so you don't have to worry that you loose them.
If you want to control protonation of histidin residues use the option -his.

Greetings
Oliver

Dinesh Pinisetty wrote:
> 
> 
> 
> 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.
> 
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-- 
Oliver Lange
MPI for biophysical Chemistry
olange at gwdg.de
Fax: +495512012302
Tel: +495512012305