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] <mailto:[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_RestraintsAs 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? MarkOn Thu, Jun 14, 2012 at 11:21 AM, Mark Abraham <[email protected] <mailto:[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]<mailto:[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] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- BharatPh.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] <mailto:[email protected]>-- gmx-users mailing list [email protected] <mailto:[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] <mailto:[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] <mailto:[email protected]>
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