[gmx-users] R: Re: rhombic dodecahedron and g_sas
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Jul 13 18:10:37 CEST 2011
Hi Anna,
That was indeed the sort of output I meant; just what g_sas is
blurting to the screen :)
Now it completely eludes me why non-rectangular boxes might give wrong
results. The code doesn't help much either. But if you want to be sure
that your results are good, you can first make the molecule whole with
trjconv, and run g_sas with the option -nopbc
Cheers,
Tsjerk
On Wed, Jul 13, 2011 at 5:08 PM, Anna Marabotti
<anna.marabotti at isa.cnr.it> wrote:
> 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)
>>
>
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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