[gmx-users] system contains proteins and DNAs with ffamber99

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jun 11 10:33:48 CEST 2008

Dechang Li wrote:
> Dear all, 
>     Sometimes,the PDB file contains water molecules which only have the oxygen atom. Can 
> Gromacs add the hydrogen atoms of the water molecules?

No - you'll be better off deleting them all, re-solvating using genbox
and then doing a normal minimization & equilibration process. An
exception might be waters in an enzyme active site or such, in which
case you're best off building the hydrogens by hand.

>     Additionly, when use Gromacs with the force field ffamber99, Can it add the hydrogen 
> atoms of the DNA? 

Yes, if there are suitable hydrogen database entries in the relevant
.hdb file. See chapter 5 of the manual for background here.

> Can I use the force field ffamber99 to simulate the system which contains
> proteins and DNAs?  

Check the contents of the .rtp file to see what "residues" are defined.


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