Re: [gmx-users] pdb2gmx doesn´t generate H

Hi, This seems to be a problem with amber ports in gromacs. I believe it is because the residue attached to an N terminal residue. Try manually adding the hydrogen to the backbone nitrogen in the SER2 in the pdb. This solved the problem for me although there were reports from other people of the

[gmx-users] Fwd: PE compressing - for reference only

Dear Moeed: Please find attached the simulation results as well as the input files for your PE system. I started the simulation from your 8PE configuration and compressed it to the density of ~890 kg/m3. It is rather good since ranges between the experimental values - http://en.wikipedia.org/wiki/

Re: [gmx-users] implicit water model for protein folding simulation

On 24/07/10 01:24, Samrat Pal wrote: I am trying to do some folding simulations in GROMACS. I saw few mails in the list stating that implicit water model will be available in GROMACS 4.0 version. However, I have not found anything on the implicit model in the manual. I am currently using GROMACS

[gmx-users] Ryckaert Bellemanm-dihedral in OPLS-AA

Dear all, I had added RB dihedrals in ffoplsaabon.itp in the following way... P O2 O2 O2 3 0.0 0.0 0.0 0.0 0.0 0.0 ; TPO CT OS CT CT_23 0.0 0.0 0.0 0.0 0.0 0.0 ; TPO CT_2 CT