[gmx-users] N-terminal hydrogen problem

[Bert de Groot]

Paul Barrett wrote:
> 
> Please can anyone help me see where I am going wrong!
> 
> -I have 2 proteins I want to simulate together.
> -either simulated by itself is fine
> -when I simulate the two proteins together the N-terminal of the second
> protein always gives this error:
> 
> Fatal error: Atom H1 in residue VAL 299 not found in rtp database
>              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.
> 
> Which is understandable because H1 doesnt exist in [VAL] in the .rtp.
> The problem is that this H1 comes from protonate which makes the
> n-terminal different to the .rtp.
> 
> HOWEVER: the N-terminal of the same protein when simulated alone works
> fine. Also in the combined simulation the N-terminal MET of the other
> protein is fine, even though it contains H1, H2 and H3 which do not
> exist in [MET] in .rtp
> 
> Maybe Im failing to signal to GROMACS that the second protein starts at
> residue 299 so it is being intolerant...
> 


right. AFAIK, pdb2gmx only recognizes multimeric pdb files correctly if
the chain identifiers in the pdb file are unique (and correct). Without
it, it will try and connect the last residue of the first chain to the first
residue of the second chain (and maybe complain about a long bond). 

--

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________