[gmx-users] N-terminal hydrogen problem

Paul Barrett barrett at biop.ox.ac.uk
Wed May 7 16:07:01 CEST 2003

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
             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...

The N terminals of the two proteins in the .gro file are included

Can anyone help me make GROMACS deal with the 2nd N-terminal in the same
way that it deals with the 1st?

many thanks

Paul Barrett
University of Oxford


    1MET      N    1   4.392   1.871   3.822
    1MET     H1    2   4.376   1.966   3.798
    1MET     H2    3   4.449   1.828   3.752
    1MET     H3    4   4.304   1.823   3.828
    1MET     CA    5   4.461   1.863   3.953

  298LEU     O1 3056   6.959   1.767   5.126
  298LEU     O2 3057   6.721   1.787   5.167
  299VAL      N 3058   6.054   5.976   3.991   ;here is the N terminal
  299VAL     H1 3059   6.083   5.972   4.087
  299VAL     H2 3060   6.114   6.038   3.941
  299VAL     H3 3061   5.960   6.009   3.986
  299VAL     CA 3062   6.063   5.838   3.931

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