Thank you David<br><br>A bientôt <br><br>SA<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Message: 1<br>
Date: Sun, 10 Apr 2011 11:17:15 +0200<br>
From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] Different g_sas values between AMBER, CHARMM<br>
and GROMOS ff for DPC<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DA1759B.2000105@xray.bmc.uu.se">4DA1759B.2000105@xray.bmc.uu.se</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 2011-04-10 11.11, sa wrote:<br>
> Thank you David,<br>
><br>
> My micelle simulated with the GROMOS ff slightly differs (size and<br>
> shape) from the two others micelles, so i expected that the values total<br>
> SAS value slightly differ. In case of the headgroup, they are located in<br>
> the micelle interface region, so the SAS in case of the micelle<br>
> simulated with GROMOS should be not so different (36 % less) than the<br>
> others micelles<br>
><br>
> You said that "In order for g_sas to work with gromos force field one<br>
> would have to<br>
> increase the radius of the carbon atoms. For the 54 atoms the default<br>
> value will be used." How to do that ? and for all the carbon atoms<br>
> (including the headgroup carbon atoms).<br>
edit vdwradii.dat.<br>
Then be careful to use an atom name that is specific for the FF such<br>
that your Amber and Charmm runs keep the correct value.<br>
><br>
> Thank you<br>
><br>
> SA<br>
><br>
><br>
> On 2011-04-09 19.06, sa wrote:<br>
> > Dear All,<br>
> ><br>
> > I have simulated three DPC micelles with the same size (54<br>
> lipids) with<br>
> > different force fields (CHARMM, AMBER et GROMOS53A6) and computed the<br>
> > average accessible surface areas for each lipids with g_sas<br>
> (gmx4.5.3) I<br>
> > obtain the three average values for total DPC, the headgroup<br>
> > (phosphocholine) and the alkyl tail.<br>
> ><br>
> > Total (A2) Head Tail<br>
> ><br>
> > GROMOS53A6 158.4 ± 4.8 54.8 ± 3.4 103.2 ± 3.8<br>
> > AMBER 248.2 ± 8.7 76.2 ± 5.1 172.5 ± 5.2<br>
> > CHARMM 242.7 ± 7.7 70.4 ± 4.1 172.4 ± 4.8<br>
> ><br>
> > As you can see the ASA values are close between the micelles<br>
> simulated<br>
> > with the CHARMM and AMBER ff, but larger than the values obtained<br>
> from<br>
> > the micelle simulated with GROMOS ff especially for the<br>
> headgroup. I am<br>
> > aware that CHARMM and AMBER are explicits ff whereas GROMOS is an<br>
> > united ff It is the reason I obtain a smaller values for GROMOS<br>
> > compared to two others ones ?<br>
> ><br>
> ><br>
> > Does g_sas tool take into account this. I have also noted when I use<br>
> > g_sas i obtain the following message<br>
> ><br>
> > WARNING: masses and atomic (Van der Waals) radii will be determined<br>
> > based on residue and atom names. These numbers can deviate<br>
> > from the correct mass and radius of the atom type.<br>
> ><br>
> > WARNING: could not find a Van der Waals radius for 54 atoms<br>
> ><br>
> > It is important ?<br>
><br>
> Given your observations above, don't you think it might be?<br>
> In order for g_sas to work with gromos force field one would have to<br>
> increase the radius of the carbon atoms. For the 54 atoms the default<br>
> value will be used.<br>
> ><br>
> > Thank you in advance for your advices.<br>
> ><br>
> > SA<br>
> ><br>
><br>
><br>
> --<br>
> David van der Spoel, Ph.D., Professor of Biology<br>
> Dept. of Cell & Molec. Biol., Uppsala University.<br>
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
><br>
><br>
<br>
<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
<br>
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