Fred, you could use the Academic version of Desmond freely available here: https://www.deshawresearch.com/resources_desmond.html The only difference from the commercial version is absence of OPLS3e force field but you still could use GPU.
вт, 4 авг. 2020 г. в 10:08, Fred Vellieux <[email protected]>: > 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/ > -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2 ######################################################################## 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/
