[gmx-users] R: Re: rhombic dodecahedron and g_sas
Anna Marabotti
anna.marabotti at isa.cnr.it
Wed Jul 13 17:08:31 CEST 2011
Dear Tsjerk,
thank you very much for your answer. What do you mean saying that I should
have provided "the exact output of g_sas"? Do you mean that I have to send
you the resulting .xvg file? If you are meaning the exact words that appear
on the screen when I launch g_sas, they are exactly what I wrote in my
previous message. However, to be more complete, I'm pasting here the screen
message:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
Michael Scharf
The Double Cube Lattice Method: Efficient Approaches to Numerical
Integration
of Surface Area and Volume and to Dot Surface Contouring of Molecular
Assemblies
J. Comp. Chem. 16 (1995) pp. 273-284
-------- -------- --- Thank You --- -------- --------
No tpr file, will not compute Delta G of solvation
Reading frame 0 time 0.000
Reading frame 0 time 10000.000
WARNING: non-rectangular boxes may give erroneous results or crashes.
Analysis based on vacuum simulations (with the possibility of evaporation)
will certainly crash the analysis.
Select a group for calculation of surface and a group for output:
Group 0 ( System) has 84335 elements
Group 1 ( Protein) has 7430 elements
Group 2 ( Protein-H) has 5826 elements
Group 3 ( C-alpha) has 718 elements
Group 4 ( Backbone) has 2154 elements
Group 5 ( MainChain) has 2874 elements
Group 6 ( MainChain+Cb) has 3562 elements
Group 7 ( MainChain+H) has 3530 elements
Group 8 ( SideChain) has 3900 elements
Group 9 ( SideChain-H) has 2952 elements
Group 10 ( Prot-Masses) has 7430 elements
Group 11 ( non-Protein) has 76905 elements
Group 12 ( Water) has 76899 elements
Group 13 ( SOL) has 76899 elements
Group 14 ( non-Water) has 7436 elements
Group 15 ( Ion) has 6 elements
Group 16 ( NA) has 6 elements
Group 17 ( Water_and_ions) has 76905 elements
Select a group: Select a group: 7430 out of 7430 atoms were classified as
hydrophobic
WARNING: if there are broken molecules in the trajectory file,
they can not be made whole without a run input file
Reading frame 1 time 10005.000
Reading frame 2 time 10010.000
Reading frame 3 time 10015.000
Reading frame 4 time 10020.000
Reading frame 5 time 10025.000
Reading frame 6 time 10030.000
Reading frame 7 time 10035.000
Reading frame 8 time 10040.000
Reading frame 9 time 10045.000
Reading frame 10 time 10050.000
Reading frame 11 time 10055.000
Reading frame 12 time 10060.000
Reading frame 13 time 10065.000
Reading frame 14 time 10070.000
Reading frame 15 time 10075.000
Reading frame 16 time 10080.000
Reading frame 17 time 10085.000
Reading frame 18 time 10090.000
Reading frame 19 time 10095.000
Reading frame 20 time 10100.000
Reading frame 30 time 10150.000
Reading frame 40 time 10200.000
Reading frame 50 time 10250.000
Reading frame 60 time 10300.000
Reading frame 70 time 10350.000
Reading frame 80 time 10400.000
Reading frame 90 time 10450.000
Reading frame 100 time 10500.000
Reading frame 110 time 10550.000
Reading frame 120 time 10600.000
Reading frame 130 time 10650.000
Reading frame 140 time 10700.000
Reading frame 150 time 10750.000
Reading frame 160 time 10800.000
Reading frame 170 time 10850.000
Reading frame 180 time 10900.000
Reading frame 190 time 10950.000
Reading frame 200 time 11000.000
Reading frame 300 time 11500.000
Reading frame 400 time 12000.000
Reading frame 500 time 12500.000
Reading frame 600 time 13000.000
Reading frame 700 time 13500.000
Reading frame 800 time 14000.000
Reading frame 900 time 14500.000
Reading frame 1000 time 15000.000
Reading frame 1100 time 15500.000
Reading frame 1200 time 16000.000
Reading frame 1300 time 16500.000
Reading frame 1400 time 17000.000
Reading frame 1500 time 17500.000
Reading frame 1600 time 18000.000
Reading frame 1700 time 18500.000
Reading frame 1800 time 19000.000
Reading frame 1900 time 19500.000
Reading frame 2000 time 20000.000
Reading frame 3000 time 25000.000
Reading frame 4000 time 30000.000
Last frame 4000 time 30000.000
Printing out areas per atom
Back Off! I just backed up atomarea.xvg to ./#atomarea.xvg.3#
gcq#163: "If You Don't Like Cool Quotes Check Your GMXRC File" (Your
Sysadmin)
In any case, if I understand well, I have to convert my .gro file (into a
.tpr file to obtain the exact value of hydrophobicity/hydrophilicity, right?
And what about the warning on possible "erroneous results" for
non-rectangular boxes? Is there a way to understand if the results are
reliable or not?
Anna
-----Messaggio originale-----
------------------------------
Message: 2
Date: Wed, 13 Jul 2011 15:54:07 +0200
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] rhombic dodecahedron and g_sas
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<CABzE1SgSguur66kG89LSMfb57on8he0dYtDxND1nrhWsXAEsqg at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi Anna,
It would have been best if you provided us the exact output of g_sas.
In any case, the classification of your atoms has nothing to do with
the type of PBC. It has to do with the fact you're using a .gro file
as a reference, which contains no charges. As a consequence, all atoms
are taken to have zero charge, and thus regarded hydrophobic.
Cheers,
Tsjerk
On Wed, Jul 13, 2011 at 2:35 PM, Anna Marabotti
<anna.marabotti at isa.cnr.it> wrote:
> Dear all,
> once again about this subject (I'm not sure I'll do another simulation in
a
> rhombic dodecahedron system...)
> I used g_sas to compute solvent accessible surface area of my system. The
> command was:
>
> g_sas -f prot_boxdodfull_mol.xtc -s prot_boxdodfull_molrenum.gro -o
> prot_boxdodfull_sas.xvg -or prot_boxdodfull_sasres
> selecting 1 (protein) for calculation and for output.
>
> I saw the following Warning message: non-rectangular boxes may give
> erroneous results or crashes. Analysis based on vacuum simulations (with
the
> possibility of evaporation) will certainly crash the analysis.
>
> In addition, there was another comment: No .tpr file, will not compute
Delta
> G of solvation.
>
> However, I tried to do my calculation.
> At the start, I saw a message saying that all the atoms of my protein were
> classified as hydrophobic (that is indeed a very strange behaviour; my
> protein is a globular protein, and certainly not all their atoms are
> hydrophobic). At the end of calculation, looking at the .xvg file with
> xmgrace -nxy, I saw indeed that hydrophobic and total SASA coincide,
whereas
> the hydrophilic area is 0 for all the time.
>
> I think this is an artifact of the non-rectangular box. Am I true? What
can
> I do? Do I have to convert my trajectory into a rectangular one? Do I have
> to forgot to calculate SASA in these conditions? Any help will be
> appreciated...
> Anna
>
> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
>
> "When a man with a gun meets a man with a pen, the man with the gun is a
> dead man"
> (Roberto Benigni, about Roberto Saviano)
>
More information about the gromacs.org_gmx-users
mailing list