Hi Fred, Have you tried http://www.charmm-gui.org/ ? I think this is the easiest way to walk through setting up input files, and you can have it generate input files for several different programs. Cheers, Alex
On Tue, Aug 4, 2020 at 4:07 AM Fred Vellieux <[email protected]> wrote: > Hello, > > I need to perform some MD calculations and then trajectories of some > small molecules analyzed. > > What I have is > 1. protein > 2. cofactor (FAD) > 3. small molecule (either single O2 atom or single Chlorine atom) > 4. crystallographic waters > > The software I can access is either Gromacs (with yum install) or > perhaps Desmond. > > I have tried and tried to get this to run (for 6 months perhaps), to no > avail. The input files located on the web do not work on the version of > Gromacs provided by the yum install command. The Maestro license > (required in order to get Desmond to run) is too expensive. > > Is there a kind soul somewhere that would have suitable input files that > would do all the above steps and who'd be willing to pass them on to me? > > What needs to be done is: > add waters to the crystallographic waters in order to fill a box of > suitable size > generate parameter and topology files for each component separately > merge these into global parameter and topology files for the system > run initial Energy Minimization > run M.D. simulations > analize the trajectories of the small molecules. > > Thanks in advance. > > Fred. > > -- > MedChem, 1st F. Medicine, Charles University > BIOCEV, Vestec, Czech Republic > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
