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

[sa]

Thank you David

A bientôt

SA


> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 10 Apr 2011 11:17:15 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Different g_sas values between AMBER,  CHARMM
>        and     GROMOS ff for DPC
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DA1759B.2000105 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>
>
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