[gmx-users] Re: Dihedral Constraints

[bharat gupta]

Thanks Sir for the reply... This question is related to my first query that
if we constraint the dihedral of the turn residue how can we fix/freeze the
movement of other residues. As I am interested in only getting the energy
of the hairpin when the turn residues are constrained within a particular
phi psi angle range....


On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 14/06/2012 12:04 PM, bharat gupta wrote:
>
>> Thanks for the reply . Is it possible to calculate the dihedral energy of
>> certain residues, like in my case for turn residues ??.. How can that be
>> done
>>
>
> First, seek to define "dihedral energy"... Force fields are not
> parametrized such that parts of them are expected to correlate with
> observables.
>
>
>
>> This another question is regarding energy minimization. Suppose, I
>> minimize the the protein solvated in water, the energy value that I get is
>> for the whole system or for the protein alone. If it's for the system then
>> how can I get the energy for the protein alone.
>>
>
> You can define energy groups (see manual) to do this for the nonbonded
> contributions. Bonded contributions are easy to do in your case. Whether
> this energy is useful for anything is quite another matter.
>
> Mark
>
> --
> 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>
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120614/93c40d74/attachment.html>