Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?

Hi Sanku, you can use APBS (Adaptive Poisson-Boltzman Solver, http://www.poissonboltzmann.org/apbs/ ). This program computes the PB equation on a single conformation, but you can write a script to calculate values over trajectory. APBS has the advances to be integrated into VMD and pymol, moreov

[gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

Dear Gromacs Users, When I use the pdb2gmx command on my protein-DNA complex, for the A chain which consists of the protein.pdb2gmx told me as follows: Processing chain 1 'A' (1222 atoms, 151 residues) There are 243 donors and 215 acceptors There are 285 hydrogen bonds Will use HISE for residue

Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

ÏéÇ« ¿× wrote: Dear Gromacs Users, When I use the pdb2gmx command on my protein-DNA complex, for the A chain which consists of the protein.pdb2gmx told me as follows: Processing chain 1 'A' (1222 atoms, 151 residues) There are 243 donors and 215 acceptors There are 285 hydrogen bonds Will us

Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

On 18/07/2011 1:41 AM, Justin A. Lemkul wrote: ÏéÇ« ¿× wrote: Dear Gromacs Users, When I use the pdb2gmx command on my protein-DNA complex, for the A chain which consists of the protein.pdb2gmx told me as follows: Processing chain 1 'A' (1222 atoms, 151 residues) There are 243 donors and 2

[gmx-users] Free Eerngy and Dispersion Correction

Hi All, if switched on, is the dispersion correction included in the dH/dlambda term? Thanks, rainer -- gmx-users mailing listgmx-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 pos

Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors

Dear Justin and Mark, Thank you very much ! --- On Mon, 7/18/11, Mark Abraham wrote: > From: Mark Abraham > Subject: Re: [gmx-users] PDB2GMX :There are 0 donors and 0 acceptors > To: "Discussion list for GROMACS users" > Date: Monday, July 18, 2011, 6:16 AM > On 18/07/2011 1:41 AM, Justin A.

[gmx-users] simulation of oligomers/monomers

Dear users, I am working on a protein which is a dimer (in the crystal structure), predicted according top PISA. and some of the homologous proteins are dimers (covalent /non-covalent) some are monomers. There has not been any literature regarding the fact that the functional unit is a dimer, ie t