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

[Paul Barrett]

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
mdrun.

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.

cheers

Paul Barrett
-------------

Protocol:

 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
>protein.
>
>> 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?
>
>
>
>-- 
>Groetjes,
>
>Anton
>  _____________ _______________________________________________________
>|             |                                                       |
>|  _   _  ___,| 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/       |
>|             | "If You See Me Getting High, Knock Me Down"           |
>|             | (Red Hot Chili Peppers)                               |
>|_____________|_______________________________________________________|
>
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