[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC
David van der Spoel
spoel at xray.bmc.uu.se
Sat Apr 9 19:29:05 CEST 2011
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.
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
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