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.
[email protected] http://folding.bmc.uu.se
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