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

James Starlight jmsstarlight at gmail.com
Mon Jun 11 10:12:27 CEST 2012


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 ?

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.


2012/6/10 Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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