[gmx-users] Questions regarding the Vacuum force field and Histidine charges

Xavier Periole x.periole at rug.nl
Wed May 4 16:08:14 CEST 2005

Joanne Hanna wrote:

>1. When i use either the GROMOS96 43a1 Forcefield (official distribution) or the GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) to convert my pdb to *.gro format, although i select the  histidines to have one additional hydrogen atom, the overall charge of the His residues after this is 0. Is this correct and if not how do you specify that the histidines should carry a +1 charge.
How did you specify the charge of the histidine ? within pdb2gmx using 
the -his option ?

>2. When i use the vacuum force field to do a simulation in vacuum the overall charge of my protein comes out at 0 (from -16) how are these charges counter balanced, and if i am wanting to do a simulation with my ligands Mg2+ and AMP (for which i have created a topology and allocated charges from a gaussian calculation) how do i deal with the charges and smoothing them to be 0.
That is what you should expect ... As far as I know the vaccum force 
field is simply a modification
of the gromos force field where the charged residues are neutralized in 
order to avoid the excess
of interaction between charged residues resulting by the absence of 
screening by the solvent.

>and 3. Which force field should I be choosing? the GROMOS96 43a1 Forcefield (official distribution) or the GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)?
The main difference is (as mentioned) on the dihedrals of alkane ... 
mostly for lipid simulations ...


 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole

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