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

Balazs Jojart jojartb at pharm.u-szeged.hu
Wed Jun 11 11:17:13 CEST 2008

Dear Dechang,
in ff03 forcfield the nucleic acid parameters are the same as in the
ff99. But ff99 forcefield for proteins is not the best choice due to
it's 'helix friendly'nature. A better choice is to choose the ff03
forcfield for protein and dna, as well.
hoe this helps.

Mark Abraham írta:
> 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.
> Mark
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