[gmx-users] g_sas strange values
and.carotti at farmchim.uniba.it
Fri Sep 26 09:43:01 CEST 2003
thanks for your answer.
I've installed Gromacs 3.1.4.(1?) on july.
I don't know why I have this problems.
I have used a trajectory in pdb file format (trjconv from a trr).
If you want I can send you (private e-mail address) the files I've used
(obviously not the whole trajectory but only 5-6 frames), so you can try
Let me know.
Thanks In Advance
----- Original Message -----
From: "David" <spoel at xray.bmc.uu.se>
To: <gmx-users at gromacs.org>
Sent: Thursday, September 25, 2003 9:26 PM
Subject: Re: [gmx-users] g_sas strange values
> On Thu, 2003-09-25 at 16:06, Andrea Carotti wrote:
> > I have a protein composed by two chains (36+247 aa).
> > I have tried to use g_sas to calculate the surface only of the light
> > chain (36aa),
> > so i've crated a group for this residues (365 atoms)and I've got a
> > middle value of 125 nm^2(for the total area).
> > This value seems to be quite constant during all the simulation.
> > I've tried to do the same calculation on some "representative"
> > structures with Sybyl and MolMol,
> > selecting the same number of residues (and atoms) and I've got a value
> > approximatively of 2000 Ang^2.
> > I think that this difference is very large. I'm doing something wrong
> > with Gromacs?
> > I hope someone can help me
> Hmm, you didn't say which version of gromacs you used, but apart from
> that I have recently compared the current CVS code to the result from
> MSMS which uses a different algorithm. The numbers were very close.
> There have been some update to the SASA calculation, I don't know
> whether they made it into 3.1.4. If not you could try the CVS code.
> > Andrea
> > #############
> > Andrea Carotti
> > Dip. Farmaco-chimico
> > Università di Bari
> > via E. Orabona, 4
> > CAP 70124
> > e-mail : and.carotti at farmchim.uniba.it
> > web: http://www.farmchim.uniba.it/samba/
> > phone: +39080/5442638
> > fax: +39080/5442230
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users