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

James Starlight jmsstarlight at gmail.com
Sun Jun 10 14:03:21 CEST 2012


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.

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 :(


2012/6/10 Justin A. Lemkul <jalemkul at vt.edu>

> On 6/10/12 3:06 AM, James Starlight wrote:
>> Justin
>> I have one extra question about parametrisation of the bond type
>> Initially I had -c-c- bond so both atoms were in the sp3 hybridization.
>> I've
>> changed bond type between that atoms to the gb_16 ( from phe ring) to
>> define
>> them as the >c=c< but during the simulation I've noticed that the bond
>> between
>> that atoms is not planar ( sp2 form) and still is in the sp3. What
>> addition
>> changees should I do in my topology to change the planarity of new bond ?
> Defining appropriate atom types will be necessary here, as well.  For a
> single bond, the atom types would be -CH2-CH2- while a double bond will
> necessarily be -CH=CH-
> Also note that with a united atom representation, it's very hard to make
> such assertions about hybridization state.  There are no hydrogens, so the
> geometry of these central carbons is not easily defined.
>  Should I make some changes ia angles term as well?
>> E.g I've found
>>   612   613   614     2    ga_13  ;
>> where 612 and 613 are the atoms wich I would like to present as the
>> rigid. I've
>> change to the ga_27 ( 120) but during simulation the bond was still in
>> sp3. What
>> I've done wrong ?
> As there are no parameters for linear C=C bonds in the Gromos force
> fields, you may have to do some parameterization yourself, particularly for
> appropriate dihedrals.  One option is to look at how these bonds are
> treated in lipid force fields like the Berger parameter set, distributed by
> Peter Tieleman's group. There are double bonds defined for lipids like POPC.
> -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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