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

sa sagmx.mail at gmail.com
Sat Apr 9 19:06:11 CEST 2011

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 ?

Thank you in advance for your advices.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110409/02252097/attachment.html>

More information about the gromacs.org_gmx-users mailing list