[gmx-users] Adding water to protein to start the simulation process

Hi User, I have a protein which I have modeled by Homology modelling. The modeled protein has no water molecules in its surrounding environment. How should I add water molecule so that I can start the simulation process? Regards Monisha -- gmx-users mailing listgmx-users@gromacs.org http://

Re: [gmx-users] Error in GROMACS installation

/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s rc/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5.4/s rc' make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/d/softwares/bioinformatics/gromacs-4.5

[gmx-users] Error in GROMACS installation

Hi All, I am installing GROMACS using cygwin. I am following the steps as mentioned : http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO *no 5, make install command give the following error in the end :* ng' Creating library file: .libs/libgmx.dll.a collect2: ld returned 1

Re: [gmx-users] Effect of pH on catalytic side

ice called H++ that can make pKa estimates > for titrating sites. Not sure how accurate it is though. It uses continuum > electrostatics that may not be accurate enough for pKa estimates (see e.g. > reviews by Warshel from 1991 and 2006). I've never used H++ myself, only > heard about

Re: [gmx-users] Effect of pH on catalytic side

Thanks Justin. I haven't find any such tutorial or exact relevant research paper. Find some paper though ( http://peds.oxfordjournals.org/content/16/12/1017.full.pdf+html ), not sure how they have done. On Tue, Mar 29, 2011 at 8:51 PM, Justin A. Lemkul wrote: > > > Monis

[gmx-users] Effect of pH on catalytic side

Friends, Need a Gromacs tutorial to find effect of pH on catalytic side. Any help? Regards -- 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 posting! Plea