[gmx-users] Summary: N-terminal hydrogen problem

Paul Barrett barrett at biop.ox.ac.uk
Thu May 8 12:41:01 CEST 2003

Thanks for your help. For the archive here is a protocol that seems to
work on a multi chained .pdb file, protonates it (through pdb2gmx)
solvates it and adds counter ions in preparation for a grompp and

The main conclusion seems to be to stay in .pdbs and away from .gros for
as long as possible if you are using multiple chains.


Paul Barrett


 pdb2gmx -f [starting .pdb file]  -p preion_topol -o pre_box.pdb -merge
    (answer no to all merge questions)

 editconf -f pre_box.pdb -o boxed.pdb -bt octahedron -box 10 -c

 genbox -cp boxed.pdb -cs -p preion_topol -o solvated.pdb

 grompp -f ~/md/mdp/mdp030506a/em -c solvated.pdb -o solvated_tpr -p
preion_topol -po boxed.pdb 

 genion -s solvated_tpr.tpr -o ioned.pdb -np 2

 pdb2gmx -f ioned.pdb -p ioned_topol -o ioned.pdb

 then grompp and mdrun in the usual way
| minimise energy

grompp -f ~/md/mdp/mdp030506a/em -c ioned.pdb -o ioned_tpr -p
ioned_topol -po mdout
mdrun -v -s ioned_tpr -o post_eqm -c post_eqm -g emlog >& em.job

>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.
>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
>.rtp file).
>> 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
>> below.
>> Can anyone help me make GROMACS deal with the 2nd N-terminal in the same
>> way that it deals with the 1st?
>  _____________ _______________________________________________________
>|             |                                                       |
>|  _   _  ___,| K. Anton Feenstra                                     |
>| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
>|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
>| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
>|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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