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. 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. )
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]
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