[gmx-users] distance restraints for alpha helix

Dear all, I am trying to rebuild the alpha helix of one the chains which got destroyed during the simulation. I found that we can do that by distance restraints. So my question what is a better way of distance restraints i.e should I restrain the hydrogen bonds of the helix or any part

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thank you David I would certainly try this way. On Mon, Feb 9, 2009 at 1:08 PM, David Mobley wrote: > Hi, > >> Thanks David, But if I just remove the Copper atom and do the >> simulation as copper is charged there would be sudden change in >> electrostatics and the protein started unfolding when

Re: [gmx-users] Free energy perturbation of Cu(I) binding

the manual but could not understand it properly and was not sure what I am doing. Please help me out here. Thank you abhigna On Tue, Feb 3, 2009 at 10:36 PM, Mark Abraham wrote: > abhigna polavarapu wrote: >> >> Thanks Mark, thats what I really wanted to do. So can you please let >

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thanks Mark, thats what I really wanted to do. So can you please let me know where I can find out the way to do position restraints and to know how these work. abhigna On Tue, Feb 3, 2009 at 10:18 PM, Mark Abraham wrote: > abhigna polavarapu wrote: >> >> Thanks David, But if I

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thanks David, But if I just remove the Copper atom and do the simulation as copper is charged there would be sudden change in electrostatics and the protein started unfolding when I ran the simulation for 10ns. So I thought perturbing the charge by little every time I can get a structure with more

[gmx-users] Fwd: Individual energies of amino acids

Hi Mark, I need to calculate the individual energies of aminoacids using Gromacs. But while using energygrps option in .mdp file for each amino acid I can only calculated the nonbonded energies of this residue. Is there a way where I can calculated the bonded interactions for each ami

[gmx-users] Individual energies of amino acids

Hi Mark, I need to calculate the individual energies of aminoacids using Gromacs. But while using energygrps option in .mdp file for each amino acid I can only calculated the nonbonded energies of this residue. Is there a way where I can calculated the bonded interactions for each ami

[gmx-users] 1-4 interaction between 160 and 164 at distance 1.573 which is larger than the 1-4 table size 1.000 nm

Hi All, I am presently doing Energy calculations of individual amino acid residues by editing the .mdp file near the energygrps option by inserting each aminoacid group. I am using 42 aminoacid Amyloid peptide and the simulation is for 10ps to extract the average energies of each aminoaci

[gmx-users] Calculating energies of peptides in protein uisng g_energy

Hi Mark, I am not getting that error before with unmodified .mdp file. Abhigna ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search be

[gmx-users] Calculating energies of amino acids in a protein using g_energy

Hi, I have to calculate the energy of each amino acid in the protein. In one of the questions in mailing list http://www.gromacs.org/pipermail/gmx-users/2001-November/000222.html I came across this and this is what exactly what i should do. Can you please explain that in a more clear way as I

[gmx-users] System is exploding

I am running a 10ns simulation on a 42 mer peptide. I am doing this for predicting the stability of the beta sheet. So I deleted a bond called the lactame bond between two amino acids Lys and Asp. So if I just create mutation at any other position in the beta sheet the mdrun crashes with an error