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

[James Starlight]

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
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>>    ==============================**__==========
>>
>>    --
>>    gmx-users mailing list gmx-users at gromacs.org <mailto:
>> gmx-users at gromacs.org>
>>    http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>>
>>    <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >
>>    Please search the archive at
>>    http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>>
>>    <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>
>> before posting!
>>    Please don't post (un)subscribe requests to the list. Use the www
>> interface
>>    or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >.
>>    Can't post? Read http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>>    <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >
>>
>>
>>
> --
> ==============================**==========
>
> 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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120608/2322e13e/attachment.html>