[gmx-users] Heavyh for ligand

Bakary N'tji Diallo diallobakary4 at gmail.com
Sun Dec 23 09:09:23 CET 2018


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:

Now this will do the Hydrogen Mass Repartitioning for the protein only, not
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?


Bakary N’tji DIALLO

PhD Student (Bioinformatics) <http://linkedin.com/in/bakarydiallo>, Research
Unit in Bioinformatics (RUBi) <https://rubi.ru.ac.za/>

Mail: diallobakary4 at gmail.com |  Skype: diallobakary4

Tel:  +27798233845 | +223 74 56 57 22 | +223 97 39 77 14

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