Sorry for the last reply, I wrote turns with different sequences wrongly, it's actually the turn with different dihedral constraints. I searched the gromacs user list , where I found this link , regarding calculation of dihedral energy of selected residues. I want to know whether this method would be useful ??
On Thu, Jun 14, 2012 at 4:16 PM, Mark Abraham <[email protected]>wrote: > On 14/06/2012 4:57 PM, bharat gupta wrote: > > I am not going to compare this with anything , I have to look for > sequences and their corresponding energies and select the lowest scoring > ones. > > > You can't compare total energies of different sequences and get a > meaningful answer. What's the difference in energy between an apple and an > orange mean? You can compare the average energy of an apple cut into pieces > with the average energy of a whole apple, but that doesn't necessarily > relate to the same quantity measured for an orange, either. There's a lot > of work in measuring a decent *free* energy difference between some states. > > > I request you to kindly elaborate on freezing some portion of the > protein. ( I am bit confused as in my case I am fixing the dihedral of turn > residues which means constraining them simultaneously I want to freeze the > other region of the protein. ) > > > You need to read the link I gave last time and use "constraints" and > "restraints" in the accepted GROMACS sense in order for people to be able > to understand your meaning clearly. There are links there to the kind of > methods that are available. I think you need to do some reading and > thinking about those :-) If you lock down all the degrees of freedom then > you can't measure anything relevant. > > > Mark > > > > On Thu, Jun 14, 2012 at 3:50 PM, Mark Abraham <[email protected]>wrote: > >> On 14/06/2012 4:38 PM, bharat gupta wrote: >> >> 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. >> >> >> >> http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints >> >> >> 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.... >> >> >> .. and with what are you going to compare those energies? And what will >> that comparison mean? >> >> Mark >> >> >> >> >> On Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham >> <[email protected]>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 [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> 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 [email protected]. >>> Can't post? Read 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 : [email protected] >> >> >> >> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> 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 [email protected]. >> Can't post? Read 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 : [email protected] > > > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 [email protected]. > Can't post? Read 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 : [email protected]
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