[gmx-users] N-terminal hydrogen problem
barrett at biop.ox.ac.uk
Thu May 8 10:49:01 CEST 2003
Yes: all this is subsequent to a protonation.
I will try the suggestions you made
>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
>> 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.
>Do I understand you correctly, that you first used protonate (Gromacs
>tool) to add hydrogens, and subsequently used pdb2gmx? That may be one
>source of problems; pdb2gmx is designed to add hydrogens according to
>the definitions in the forcefield you choose (i.e. the corresponding
>> 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...
>Adding a 'TER' line in your pdb file doesn't help, unfortunately. This
>is a shortcoming of pdb2gmx that should be fixed. In the meantime you
>will need to add explicit chain identifiers, e.g. 'A' for your first
>chain and 'B' for the second. Easiest is to use editconf, it has an
>option to add a chain identifier. You can either first label the two
>separate pdb files and then merge them, or label the merged file, and
>then use an editor to replace the 'A' label with 'B' for the second
>> 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?
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>| _ _ ___,| K. Anton Feenstra |
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