[gmx-users] Heavyh for ligand

Dallas Warren dallas.warren at monash.edu
Wed Jan 2 01:11:34 CET 2019


Adjust masses by hand.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Sun, 23 Dec 2018 at 19:09, Bakary N'tji Diallo <diallobakary4 at gmail.com>
wrote:

> 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: diallobakary4 at gmail.com |  Skype: diallobakary4
>
> Tel:  +27798233845 | +223 74 56 57 22 | +223 97 39 77 14
> --
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