Thank you David A bientôt
SA > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 10 Apr 2011 11:17:15 +0200 > From: David van der Spoel <[email protected]> > Subject: Re: [gmx-users] Different g_sas values between AMBER, CHARMM > and GROMOS ff for DPC > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > 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. > > [email protected] <mailto:[email protected]> > > 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. > [email protected] http://folding.bmc.uu.se > > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 84, Issue 80 > ***************************************** >
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