Hello I am interested in running a simulation of protein-ligand complex to assess their stability and using the Hydrogen Mass Repartitioning <https://pubs.acs.org/doi/10.1021/ct5010406> technique. I am doing so by using the "-heavyh" option of pdb2gmx. the option will "increase the hydrogen-mass by a factor of 4. This is also done for water hydrogens to slow down the rotational motion of water. The increase in mass of the hydrogens is subtracted from the bonded (heavy) atom so that the total mass of the system remains the same.". See manual: http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-pdb2gmx.html
Now this will do the Hydrogen Mass Repartitioning for the protein only, not ligand. The topology for the ligand is being generated using acpype. I have checked the mass of atoms for the protein and the ligand and they are different. How can I fix that for the ligand? Thanks -- Bakary N’tji DIALLO PhD Student (Bioinformatics) <http://linkedin.com/in/bakarydiallo>, Research Unit in Bioinformatics (RUBi) <https://rubi.ru.ac.za/> Mail: diallobaka...@gmail.com | Skype: diallobakary4 Tel: +27798233845 | +223 74 56 57 22 | +223 97 39 77 14 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
