[gmx-users] free energy calculation and g_bar error

Dear gmx-users: I was trying to do a free energy calculation of a charged ligand, according to the paper "Calculation of Absolute Binding Free Energies for Charged Ligands and Effects of Long-Range Electrostatic Interactions ", one of the problems with charged ligands is that the use of a sol

[gmx-users] Re: Re: couple-moltype of FEP (Justin A. Lemkul)

Dear Justin: What I mean is can I calculate the free energy of restraining the ligand in the binding site, since I put on distance restraint to the ligand and the protein? Regards Chunxia Chunxia Gao wrote: > Dear Justin, > > If I apply the pull code to the distance restraints, can I

[gmx-users] free energy calculation " State B has non-zero total charge: 5.800000e+01 "

Dear gmx users: I am using the free energy to calculate the ligand binding affinity to protein, during the decouple process, I need to put some restraint between the protein and the ligand, e.g. distance restraint. But distance restraint is only for intramolecular, so I need to make a hybrid

[gmx-users] what's the parameters for angle restraints in mdp file

Dear gmx users: Do anybody know what is the parameters for angle restraints in mdp file, like distance restraint it will have like disre = simple and dihedral restraints will have dihre = yes, and what about for angle restraints? nothing? just defined the force constant and that atom index in t

[gmx-users] orientation restraints in binding free energy calculation

Dear gmx-users: I read some research articles of calculating the binding free energy, still I can not figure out how to get the orientational parameters. If I have the crystal structure of ligand bound protein, so I need to choose three anchor atoms in the protein and three anchor atoms in the

[gmx-users] RE:RE: gromacs installation

e step "./configure", maybe you should use "./configure --prefix=/home/yourname/..." to change the default installation directory. Just my two cents. Hope it helps. --hualin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] O

[gmx-users] gromacs installation

Dear all: I was wondering did any one try to install the gromacs 4.5.X in your own account of supercomputer cluster? I tried to do this, and I had some error messages showed up. First, for fftw installation, I did ./configure --enable-threads --enable-float --prefix=/home/chunxia/fftw make mak

[gmx-users] grompp error

Dear all, I generated the molecule topology from antechamber and then coverted to gromcas topology. When I tried to use grompp first it gave me this error : there is no such molecule type SOL, so I checked the topology file and found out there was no #include "tip3p.itp" . so I added this to