[gmx-users] N-terminal hydrogen problem
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?
University of Oxford
FIRST PROTEIN N-TERMINAL
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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