[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC

[David van der Spoel]

On 2011-04-10 11.11, sa wrote:
> Thank you David,
>
> My micelle simulated with the GROMOS ff slightly differs (size and
> shape) from the two others micelles, so i expected that the values total
> SAS value slightly differ. In case of the headgroup, they are located in
> the micelle interface region, so the SAS in case of the micelle
> simulated with GROMOS should be not so different (36 % less) than the
> others micelles
>
> You said that "In order for g_sas to work with gromos force field one
> would have to
> increase the radius of the carbon atoms. For the 54 atoms the default
> value will be used." How to do that ? and for all the carbon atoms
> (including the headgroup carbon atoms).
edit vdwradii.dat.
Then be careful to use an atom name that is specific for the FF such 
that your Amber and Charmm runs keep the correct value.
>
> Thank you
>
> SA
>
>
>     On 2011-04-09 19.06, sa wrote:
>      > Dear All,
>      >
>      > I have simulated three DPC micelles with the same size (54
>     lipids) with
>      > different force fields (CHARMM, AMBER et GROMOS53A6) and computed the
>      > average accessible surface areas for each lipids with g_sas
>     (gmx4.5.3) I
>      > obtain the three average values for total DPC, the headgroup
>      > (phosphocholine) and the alkyl tail.
>      >
>      >            Total (A2)        Head          Tail
>      >
>      > GROMOS53A6    158.4 ± 4.8     54.8 ± 3.4         103.2 ± 3.8
>      > AMBER              248.2 ± 8.7     76.2 ± 5.1         172.5 ± 5.2
>      > CHARMM           242.7 ± 7.7     70.4 ± 4.1          172.4 ± 4.8
>      >
>      > As you can see the ASA values are close between the micelles
>     simulated
>      > with the CHARMM and AMBER ff, but larger than the values obtained
>     from
>      > the micelle simulated with GROMOS ff especially for the
>     headgroup. I am
>      > aware that  CHARMM and AMBER are explicits ff whereas GROMOS is an
>      > united ff  It is the reason I obtain a smaller values for GROMOS
>      > compared to two others ones ?
>      >
>      >
>      > Does g_sas tool take into account this. I have also noted when I use
>      > g_sas i obtain the following message
>      >
>      > WARNING: masses and atomic (Van der Waals) radii will be determined
>      >           based on residue and atom names. These numbers can deviate
>      >           from the correct mass and radius of the atom type.
>      >
>      > WARNING: could not find a Van der Waals radius for 54 atoms
>      >
>      > It is important ?
>
>     Given your observations above, don't you think it might be?
>     In order for g_sas to work with gromos force field one would have to
>     increase the radius of the carbon atoms. For the 54 atoms the default
>     value will be used.
>      >
>      > Thank you in advance for your advices.
>      >
>      > SA
>      >
>
>
>     --
>     David van der Spoel, Ph.D., Professor of Biology
>     Dept. of Cell & Molec. Biol., Uppsala University.
>     Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se