[gmx-users] Questions regarding the Vacuum force field andHistidine charges
J.F.Hanna at warwick.ac.uk
Wed May 4 16:27:59 CEST 2005
Thanks for your reply
Regarding th Histidine question I specified it using -inter, I have also done this without specifing the type of histidines and it still gives the same result.
Also would you know how i could alter the charges in the topologies that i have built myself in order to use these ligands in my vacuum calculation.
>>> x.periole at rug.nl 05/04/05 15:17 PM >>>
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
9747 AG Groningen
email: x.periole at rug.nl
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