[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC
sagmx.mail at gmail.com
Sat Apr 9 19:06:11 CEST 2011
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
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 ?
Thank you in advance for your advices.
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