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

[James Starlight]

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 ?


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 ?

James

2012/6/8 James Starlight <jmsstarlight at gmail.com>

> Justin,
>
>
>
> thanks alot. I'll try to use gb_10 ( for C=N) as well as gb_16 ( for C=C)
> for parametrisation in my task.
>
>
>
> James
>
> 2012/6/8 Justin A. Lemkul <jalemkul at vt.edu>
>
>>
>>
>> On 6/8/12 2:01 PM, James Starlight wrote:
>>
>>> Justin,
>>>
>>> Does the gb_10 suitable for both bonds that I want to parametrise ?
>>>
>>> As I've told previously I need to parametrise two different bonds
>>>
>>> 1) is the >C=C< bond wich are not in the ring. This is just double bound
>>> in
>>> linnear sequence -C=C-.
>>>
>>> 2) is the >C=N- double bond where both atoms in the 5-m ring system
>>>
>>>
>> This is a better description.  The last message suggested everything was
>> in a 5-membered ring.  Had that been the case, my suggestion would have
>> been right (see, for instance, a HIS side chain - gb_10 is used for both
>> C=C and C=N in that case).
>>
>> There are no linear C=C bonds in Gromos force fields by default, as such
>> groups are not in proteins.  The closest you can likely come is to take a
>> C=C bond from the PHE ring.  Bond lengths are simple, and are usually
>> derived from spectroscopic information.  If using constraints on all bonds,
>> the force constant is irrelevant since the bond is rigid.  If not using
>> constraints, then you'll have to find or derive suitable parameters
>> yourself.  Welcome to the inconvenient world of parameterization :)
>>
>> -Justin
>>
>>  Thanks again,
>>>
>>> James
>>>
>>>
>>>
>>> 2012/6/8 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>>
>>>
>>>
>>>
>>>    On 6/8/12 1:22 PM, James Starlight wrote:
>>>
>>>        I've found that information in ffbonded.itp but I'm not sure
>>> about exactly
>>>        meaning of some types.
>>>
>>>
>>>        E.g I'm looking for bond type for simple double bond between C=C
>>> as well
>>>        as C=N
>>>        ( here both atoms in 5-m ring) atoms pairs. Should I use for the
>>> first one
>>>        #define gb_15       0.1390  8.6600e+06
>>>        ; CH2  -  C, CR1 (6-ring)       800
>>>
>>>           and for the second one ;
>>>
>>>        #define gb_11       0.1340  1.0500e+07
>>>        ; C  -  N, NZ, NE       900
>>>        ?
>>>
>>>
>>>    Neither.  gb_10 sounds exactly like what you need:
>>>
>>>    #define gb_10       0.1330  1.1800e+07
>>>    ; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)       1000
>>>
>>>    -Justin
>>>
>>>    --
>>>    ==============================**__==========
>>>
>>>
>>>    Justin A. Lemkul, Ph.D.
>>>    Research Scientist
>>>    Department of Biochemistry
>>>    Virginia Tech
>>>    Blacksburg, VA
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>> --
>> ==============================**==========
>>
>> 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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