[gmx-users] parameters for bond types for GROMOS force field.

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jun 11 10:27:33 CEST 2012

On 11/06/2012 6:12 PM, James Starlight wrote:
> Justin
> 1) So if I understood correctly I can make parametrisation of my 
> uncommon group by the atb for instance. Than I can change itp file to 
> rtp form and integrate this new residue to the existing ff. Finally 
> when I will run pdb2gmx on the protein with the same group (even with 
> different atom order) I obtain proper topology.top file. Doest it 
> correct ?

The "change" to which you refer will be non-trivial because of the 
covalent bond. Charge distribution and atom types will change.

> 2) I've defined bond between both of my atoms as the  gb_15 and define 
> this atoms as the C in the topology.top. Than I've run minimisation 
> and short 3ns MD_run. Unfortunatelly this atoms was in the sp3 form 
> and were not in the planar form :(  What else should I do ? Could some 
> operations with the angle term in topology.top help me? I've modified  
> 612   613   614     2 as the    ga_27   but it also could not help me.

It is possible to hack something that will work, but the transferability 
of charges from an isolated form to a form covalently bound to a peptide 
is (at best) doubtful. If your atomic arrangement is changing, the 
presence of single vs double bonds must be changing, and that should 
basically guarantee non-transferability.

The most correct form of a solution is to parameterise the modified form 
of the residue along the same lines as the original force field 
parameterization. That may or may not be feasible for you. It's hard to 
be more specific without knowing exactly what modified residue you are 
seeking to create.


> James
> 2012/6/10 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     On 6/10/12 8:03 AM, James Starlight wrote:
>         Justin,
>         thanks again for help.
>         Finally is there any generall solution to parametrise
>         hetero-groups covalently
>         bonded with the protein ? Many proteins consist of such groups
>         e.g chromophore
>         in GFP, retinall in rhodopsin as well as some prostetic groups
>         in the enzymes.
>     Parameterization schemes differ across force fields.  It's never
>     easy.
>         I've tried to make something like you've told me via inclusion of
>         pre-parametrised residues in the existing gromacs ff but
>         forced with some
>         problems due to the atom order in new ITP and gro files
>         provided by ATb or
>         PRODRG are different from initial pdb file so pdb2gmx on the
>         whole protein where
>         het-group in the old order would not work properly :(
>     The output .itp files of ATB or PRODRG are not what you should be
>     using.  You can't #include a covalently attached residue and
>     expect the resulting dynamics to be relevant; it's not like a ligand.
>     What you need to do in those cases is create an .rtp entry (and
>     any other incidental bonded and nonbonded additions, as stated
>     before) that specifies whatever parameters you believe to be
>     reliable.  At that point, when the .rtp file is read, the atom
>     order is irrelevant - if pdb2gmx finds the atoms it needs, it
>     builds the topology.
>     -Justin
>     -- 
>     ========================================
>     Justin A. Lemkul, Ph.D.
>     Research Scientist
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>     ========================================
>     -- 
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