Hi, This query is related to my previous queries. I want to constraint the psi/psi angle of the turn residue of my beta-hairpin , meaning that they are allowed to move in certain range of psi/phi angle space. Simultaneously, I want to freeze the movement of strand residues. This procedure has to be followed during minimization alone. From the previous answers to my queries I understood how to constrain dihedral space, but I don't know how to fix the movement of strand residues ?? ... any help will be highly appreciated.
On Thu, Jun 14, 2012 at 4:24 PM, bharat gupta <bharat.85.m...@gmail.com>wrote: > 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 <mark.abra...@anu.edu.au>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 <mark.abra...@anu.edu.au>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 >>> <mark.abra...@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@gromacs.org >>>> 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 gmx-users-requ...@gromacs.org. >>>> 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 : monu46...@yahoo.com >>> >>> >>> >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> 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 : monu46...@yahoo.com >> >> >> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> 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 : monu46...@yahoo.com > > -- 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 : monu46...@yahoo.com
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