[gmx-users] Re:Help: Analysis large interdomain motion

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 25 08:51:12 CEST 2005


On Mon, 2005-04-25 at 08:47 +0800, Zhenting Gao wrote:
> Hi  gmx-users ,
> 
> Thanks a lot to  Oliver Beckstein, Karsten Suhre, and T.A.Wassenaar.
> Your suggestion are mainly about how to define the interdomain motion. 
> And I want to go a step further, and I want to know generally what is the reason of large interdomain motion, ie. the force and critical aminoacids etc..
> 
> Is there any general idea on this, or some papers talking this? 
check papers by steve hayward and herman berendsen, there is curr. op.
struct. biol. by them a few years back.
> 
> 
> 
> ======= 2005-04-21, 11:12:56 2005-04-21, 11:12:56 you wrote:=======      
> 
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> >Today's Topics: 
> > 
> >   1. Re: Help: Analysis large interdomain motion (Oliver Beckstein) 
> >   2. lateral diffusion  (Arvid Soderhall) 
> >   3. potential energy (Michal Kolinski) 
> >   4. g_anaeig '-s' option (Sichun Yang) 
> >   5. Bob Arenburg/Austin/IBM is out of the office. (Bob Arenburg) 
> >   6. editconf errors for isoleucine residue (YOLANDA SMALL) 
> > 
> > 
> >---------------------------------------------------------------------- 
> > 
> >Message: 1 
> >Date: Wed, 20 Apr 2005 13:09:45 +0100 (BST) 
> >From: Oliver Beckstein  
> >Subject: Re: [gmx-users] Help: Analysis large interdomain motion 
> >To: Discussion list for GROMACS users  
> >Cc: Paul Barrett  
> >Message-ID:  
> >Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed 
> > 
> >Adding to the discussion on NMA, protein motions, visualisation and such: 
> > 
> >A colleague of mine, Dr Paul Barrett, set up a web service called 
> >'Dynamite' at 
> > 
> >  http://dynamite.biop.ox.ac.uk/dynamite 
> > 
> >Amongst other things, it produces PCA of protein ensembles based on Bert 
> >de Groot's CONCOORD and visualises them nicely as 'porcupine plots' (the 
> >arrows sticking out from the backbone). 
> > 
> >You can also analyse xtc trajectories of your own. 
> > 
> >Have a look at the site, read the available documentation, and contact 
> >Paul (address on the website) if there are any further questions. 
> > 
> >Best wishes, 
> >Oliver 
> > 
> >On Tue, 19 Apr 2005, T.A.Wassenaar wrote: 
> > 
> >> 
> >> Hi Zhenting Gao, 
> >> 
> >> Actually, this is not uncommon. The analysis you probably want to perform 
> >> here includes principal components analysis and subsequently running the 
> >> program DynDom to reveal the nature of interdomain motions. From what you 
> >> mention you might also be interested in visualization of the loadings of the 
> >> principal components, though that has not been added to gromacs yet. 
> >> 
> >> Cheers, 
> >> 
> >> Tsjerk 
> >> 
> >> On Tue, 19 Apr 2005 19:44:23 +0800 
> >> "Zhenting Gao"  wrote: 
> >>> Hi  gmx-users , 
> >>> I am currently working on a protein with 3 domains: left, middle and right 
> >>> domain. 
> >>> While the 3 domains' internal structure remain almost unchanged(rmsd of 
> >>> each domain is below 2.5A if fit to itself), the interdomain motion between 
> >>> the left and right domains are comparably large, i.e. the rmsd of right 
> >>> domain is more than 12A if fit to the hydrolase domain. 
> >>> 
> >>> Does anyone know a protein like this? As I concern mostly at the residues 
> >>> which are indispensable for the large interdomain motion, what can I do to 
> >>> persue this? 
> >>> 
> >>> Any suggestion or papers are heartily appreciated. 
> >>> 
> >>> Yours sincerely,   Zhenting Gao   zhentg at 163.com    2005-4-19 
> >>> ------------------------------------   Drug Discovery and Design Center, 
> >>> Shanghai Institute of Materia Medica,   Chinese Academy of Science 
> >>> P.R.China   http://www.dddc.ac.cn/group/zhentg.htm 
> >>> 
> >>> 
> >>> 
> >>> _______________________________________________ 
> >>> gmx-users mailing list 
> >>> gmx-users at gromacs.org 
> >>> http://www.gromacs.org/mailman/listinfo/gmx-users 
> >>> Please don't post (un)subscribe requests to the list. Use the www interface 
> >>> or send it to gmx-users-request at gromacs.org. 
> >> 
> >> _______________________________________________ 
> >> gmx-users mailing list 
> >> gmx-users at gromacs.org 
> >> http://www.gromacs.org/mailman/listinfo/gmx-users 
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> >> 
> >> 
> > 
> >-- 
> >Oliver Beckstein * oliver at biop.ox.ac.uk 
> >  http://sansom.biop.ox.ac.uk/oliver/ 
> > 
> > 
> > 
> >------------------------------ 
> > 
> >Message: 2 
> >Date: Wed, 20 Apr 2005 15:30:39 +0200 
> >From: Arvid Soderhall  
> >Subject: [gmx-users] lateral diffusion  
> >To: "gmx-users at gromacs.org"  
> >Message-ID: <4266597F.2010904 at fmp-berlin.de> 
> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed 
> > 
> >Dear all 
> >I have a  question concerning the calculation of lateral diffusion in a  
> >lipid bilayer: How to remove the apparent supradiffusivity of the two  
> >monolayers in the g_msd calculation? Is it just to calculate the lateral  
> >diffusion of each monolayer sepately and then take the average??? 
> > 
> >Arvid SAerhl 
> > 
> > 
> > 
> >------------------------------ 
> > 
> >Message: 3 
> >Date: Wed, 20 Apr 2005 17:40:42 +0200 
> >From: "Michal Kolinski"  
> >Subject: [gmx-users] potential energy 
> >To:  
> >Message-ID: <000e01c545bf$4f61d990$be01000a at hades> 
> >Content-Type: text/plain; charset="iso-8859-2" 
> > 
> >Hi all. 
> >I did 2ns MD  of system involving TM-protein + ligand + lipids + SOL + ions. 
> >How can I  calculate potential energy separately for protein and separately  for ligand? 
> > 
> >I used PME during my simulation. 
> >My energy groups are:  protein, Mol,  DPPC, Na, SOL 
> >G_energy gives potential energy of whole system, so in order to get potential  
> >energy for separate molecule I need to add up all the necessary terms? (from g_energy 
> >output).   How can I calculate LR Coulomb energies for each of the defined groups? 
> >Is there any easy way to get potential energy for defined group? 
> >Thank you in advance.  
> > 
> >  
> > 
> >   1=          Bond   2=         Angle   3=   Proper Dih.   4=Ryckaert-Bell. 
> >   5= Improper Dih.   6=         LJ-14   7=    Coulomb-14   8=       LJ (SR) 
> >   9=  Coulomb (SR)  10=  Coulomb (LR)  11=     Potential  12=   Kinetic En. 
> >  13=  Total Energy  14=   Temperature  15=Pressure (bar)  16=         Box-X 
> >  17=         Box-Y  18=         Box-Z  19=        Volume  20=  Density (SI) 
> >  21=            pV  22=        Vir-XX  23=        Vir-XY  24=        Vir-XZ 
> >  25=        Vir-YX  26=        Vir-YY  27=        Vir-YZ  28=        Vir-ZX 
> >  29=        Vir-ZY  30=        Vir-ZZ  31= Pres-XX (bar)  32= Pres-XY (bar) 
> >  33= Pres-XZ (bar)  34= Pres-YX (bar)  35= Pres-YY (bar)  36= Pres-YZ (bar) 
> >  37= Pres-ZX (bar)  38= Pres-ZY (bar)  39= Pres-ZZ (bar)  40= #Surf*SurfTen 
> >  41=  Pcoupl-Mu-XX  42=  Pcoupl-Mu-YY  43=  Pcoupl-Mu-ZZ  44=          Mu-X 
> >  45=          Mu-Y  46=          Mu-Z  47=Coul-SR:DPPC-DPPC  48=  LJ:DPPC-DPPC 
> >  49=Coul-LR:DPPC-DPPC  50=Coul-14:DPPC-DPPC  51=LJ-14:DPPC-DPPC  52=Coul-SR:DPPC-Protein 
> >  53=LJ:DPPC-Protein  54=Coul-LR:DPPC-Protein  55=Coul-14:DPPC-Protein  56=LJ-14:DPPC-Protein 
> >  57=Coul-SR:DPPC-SOL  58=   LJ:DPPC-SOL  59=Coul-LR:DPPC-SOL  60=Coul-14:DPPC-SOL 
> >  61=LJ-14:DPPC-SOL  62=Coul-SR:DPPC-MOL  63=   LJ:DPPC-MOL  64=Coul-LR:DPPC-MOL 
> >  65=Coul-14:DPPC-MOL  66=LJ-14:DPPC-MOL  67=Coul-SR:DPPC-Cl  68=    LJ:DPPC-Cl 
> >  69=Coul-LR:DPPC-Cl  70=Coul-14:DPPC-Cl  71= LJ-14:DPPC-Cl  72=Coul-SR:Protein-Protein 
> >  73=LJ:Protein-Protein  74=Coul-LR:Protein-Protein  75=Coul-14:Protein-Protein  76=LJ-14:Protein-Protein 
> >  77=Coul-SR:Protein-SOL  78=LJ:Protein-SOL  79=Coul-LR:Protein-SOL  80=Coul-14:Protein-SOL 
> >  81=LJ-14:Protein-SOL  82=Coul-SR:Protein-MOL  83=LJ:Protein-MOL  84=Coul-LR:Protein-MOL 
> >  85=Coul-14:Protein-MOL  86=LJ-14:Protein-MOL  87=Coul-SR:Protein-Cl  88= LJ:Protein-Cl 
> >  89=Coul-LR:Protein-Cl  90=Coul-14:Protein-Cl  91=LJ-14:Protein-Cl  92=Coul-SR:SOL-SOL 
> >  93=    LJ:SOL-SOL  94=Coul-LR:SOL-SOL  95=Coul-14:SOL-SOL  96= LJ-14:SOL-SOL 
> >  97=Coul-SR:SOL-MOL  98=    LJ:SOL-MOL  99=Coul-LR:SOL-MOL 100=Coul-14:SOL-MOL 
> > 101= LJ-14:SOL-MOL 102=Coul-SR:SOL-Cl 103=     LJ:SOL-Cl 104=Coul-LR:SOL-Cl 
> > 105=Coul-14:SOL-Cl 106=  LJ-14:SOL-Cl 107=Coul-SR:MOL-MOL 108=    LJ:MOL-MOL 
> > 109=Coul-LR:MOL-MOL 110=Coul-14:MOL-MOL 111= LJ-14:MOL-MOL 112=Coul-SR:MOL-Cl 
> > 113=     LJ:MOL-Cl 114=Coul-LR:MOL-Cl 115=Coul-14:MOL-Cl 116=  LJ-14:MOL-Cl 
> > 117= Coul-SR:Cl-Cl 118=      LJ:Cl-Cl 119= Coul-LR:Cl-Cl 120= Coul-14:Cl-Cl 
> > 121=   LJ-14:Cl-Cl 122=        T-DPPC 123=     T-Protein 124=         T-SOL 
> > 125=         T-MOL 126=          T-Cl 127=     Lamb-DPPC 128=  Lamb-Protein 
> > 129=      Lamb-SOL 130=      Lamb-MOL 131=       Lamb-Cl 
> > 
> >-------------- next part -------------- 
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> > 
> >------------------------------ 
> > 
> >Message: 4 
> >Date: Wed, 20 Apr 2005 11:54:46 -0700 (PDT) 
> >From: Sichun Yang  
> >Subject: [gmx-users] g_anaeig '-s' option 
> >To: gmx-users at gromacs.org 
> >Message-ID:  
> >Content-Type: TEXT/PLAIN; charset=US-ASCII 
> > 
> > 
> >Hi- 
> > 
> >I have a question about the "-s" option.  
> > 
> >I used the the same structure for both -s and -f inputs, 
> >and then the 1st and 2nd projections are zero for this structure. 
> >What is the point for '-s'? why did I get zero for that? 
> > 
> >Any ideas will help. 
> > 
> >-Sichun   
> > 
> > 
> > 
> >------------------------------ 
> > 
> >Message: 5 
> >Date: Wed, 20 Apr 2005 17:41:49 -0600 
> >From: Bob Arenburg  
> >Subject: [gmx-users] Bob Arenburg/Austin/IBM is out of the office. 
> >To: Discussion list for GROMACS users  
> >Message-ID: 
> > 
> >Content-Type: text/plain; charset="us-ascii" 
> > 
> > 
> > 
> > 
> > 
> >I will be out of the office starting  04/20/2005 and will not return until 
> >04/25/2005. 
> > 
> >If you need assistance please contact Brad Elkin at be at us.ibm.com 
> >-------------- next part -------------- 
> >An HTML attachment was scrubbed... 
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> > 
> >------------------------------ 
> > 
> >Message: 6 
> >Date: Wed, 20 Apr 2005 22:59:06 -0400 (EDT) 
> >From: "YOLANDA SMALL"  
> >Subject: [gmx-users] editconf errors for isoleucine residue 
> >To: gmx-users at gromacs.org 
> >Message-ID: <200504210259.WAA09303 at webmail3.cac.psu.edu> 
> >Content-Type: text/plain 
> > 
> >Hello, 
> > 
> >I used the editconf utility to convert a file from pdb to gro and back to pdb 
> >again.  There appears to be an error in converting the units and it only 
> >happens with the isoleucine residue on a 365 residue protein.  The .gro file is 
> >using the digits after the decimal so perhaps the unit conversion part of the 
> >code is malfunctioning.  I have attached the section of the files for you to 
> >see. Is this a known problem? Has anyone else encounterd this problem? Is there 
> >a fix for it? 
> > 
> >Thanks, 
> >Yolanda 
> > 
> >>From original pdb file 
> >ATOM   1370  N   ILE A  89      48.865  40.003  13.593  1.00  0.00            
> >ATOM   1371  CA  ILE A  89      49.550  38.952  12.846  1.00  0.00            
> >ATOM   1372  C   ILE A  89      48.833  37.610  13.056  1.00  0.00            
> >ATOM   1373  O   ILE A  89      48.208  37.380  14.095  1.00  0.00            
> >ATOM   1374  CB  ILE A  89      51.052  38.899  13.240  1.00  0.00            
> >ATOM   1375  CG1 ILE A  89      51.329  38.529  14.720  1.00  0.00            
> >ATOM   1376  CG2 ILE A  89      51.766  40.205  12.847  1.00  0.00           
> >ATOM   1377  CD  ILE A  89      52.802  38.195  14.994  1.00  0.00            
> >ATOM   1378  H   ILE A  89      48.697  39.833  14.579  1.00  0.00            
> >ATOM   1379  HA  ILE A  89      49.487  39.162  11.777  1.00  0.00            
> >ATOM   1380  HB  ILE A  89      51.492  38.112  12.623  1.00  0.00            
> >ATOM   1381 HG11 ILE A  89      51.006  39.339  15.376  1.00  0.00            
> >ATOM   1382 HG12 ILE A  89      50.739  37.661  15.013  1.00  0.00            
> >ATOM   1383 HG21 ILE A  89      52.840  40.052  12.752  1.00  0.00            
> >ATOM   1384 HG22 ILE A  89      51.410  40.580  11.889  1.00  0.00            
> >ATOM   1385 HG23 ILE A  89      51.590  40.992  13.581  1.00  0.00            
> >ATOM   1386  HD1 ILE A  89      53.157  37.399  14.339  1.00  0.00            
> >ATOM   1387  HD2 ILE A  89      53.444  39.064  14.848  1.00  0.00            
> >ATOM   1388  HD3 ILE A  89      52.934  37.859  16.021  1.00  0.00 
> > 
> > 
> >Gro file generated with (editconf -f file.pdb -o file1.gro) 
> >   89ILE      N 1371  86.500   0.300  59.300 
> >   89ILE      H 1372  69.700  83.300  57.900 
> >   89ILE     CA 1373  55.000  95.200  84.600 
> >   89ILE     HA 1374  48.700  16.200  77.700 
> >   89ILE     CB 1375   5.200  89.900  24.000 
> >   89ILE     HB 1376  49.200  11.200  62.300 
> >   89ILE    CG1 1377  32.900  52.900  72.000 
> >   89ILE   HG11 1378   0.600  33.900  37.600 
> >   89ILE   HG12 1379  73.900  66.100   1.300 
> >   89ILE    CG2 1380  76.600  20.500  84.700 
> >   89ILE   HG21 1381  84.000   5.200  75.200 
> >   89ILE   HG22 1382  41.000  58.000  88.900 
> >   89ILE   HG23 1383  59.000  99.200  58.100 
> >   89ILE     CD 1384  80.200  19.500  99.400 
> >   89ILE    HD1 1385  15.700  39.900  33.900 
> >   89ILE    HD2 1386  44.400   6.400  84.800 
> >   89ILE    HD3 1387  93.400  85.900   2.100 
> >   89ILE      C 1388  83.300  61.000   5.600 
> >   89ILE      O 1389  20.800  38.000   9.500 
> > 
> >PDB file generated with (editconf -f file1.gro -o file2.pdb) 
> >ATOM   1371  N   ILE    89     865.000   3.000 593.000  1.00  0.00 
> >ATOM   1372  H   ILE    89     697.000 833.000 579.000  1.00  0.00 
> >ATOM   1373  CA  ILE    89     550.000 952.000 846.000  1.00  0.00 
> >ATOM   1374  HA  ILE    89     487.000 162.000 777.000  1.00  0.00 
> >ATOM   1375  CB  ILE    89      52.000 899.000 240.000  1.00  0.00 
> >ATOM   1376  HB  ILE    89     492.000 112.000 623.000  1.00  0.00 
> >ATOM   1377  CG1 ILE    89     329.000 529.000 720.000  1.00  0.00 
> >ATOM   1378 HG11 ILE    89       6.000 339.000 376.000  1.00  0.00 
> >ATOM   1379 HG12 ILE    89     739.000 661.000  13.000  1.00  0.00 
> >ATOM   1380  CG2 ILE    89     766.000 205.000 847.000  1.00  0.00 
> >ATOM   1381 HG21 ILE    89     840.000  52.000 752.000  1.00  0.00 
> >ATOM   1382 HG22 ILE    89     410.000 580.000 889.000  1.00  0.00 
> >ATOM   1383 HG23 ILE    89     590.000 992.000 581.000  1.00  0.00 
> >ATOM   1384  CD  ILE    89     802.000 195.000 994.000  1.00  0.00 
> >ATOM   1385  HD1 ILE    89     157.000 399.000 339.000  1.00  0.00 
> >ATOM   1386  HD2 ILE    89     444.000  64.000 848.000  1.00  0.00 
> >ATOM   1387  HD3 ILE    89     934.000 859.000  21.000  1.00  0.00 
> >ATOM   1388  C   ILE    89     833.000 610.000  56.000  1.00  0.00 
> >ATOM   1389  O   ILE    89     208.000 380.000  95.000  1.00  0.00 
> > 
> > 
> > 
> >------------------------------ 
> > 
> >_______________________________________________ 
> >gmx-users mailing list 
> >gmx-users at gromacs.org 
> >http://www.gromacs.org/mailman/listinfo/gmx-users 
> > 
> > 
> >End of gmx-users Digest, Vol 12, Issue 33 
> >***************************************** 
> > 
>       
> 
> = = = = = = = = = = = = = = = = = = = =      
>            
>                 
> 
> Yours sincerely,      
> Zhenting Gao      
> zhentg at 163.com       
> 2005-4-21       
> 
> ------------------------------------      
> Drug Discovery and Design Center,      
> Shanghai Institute of Materia Medica,      
> Chinese Academy of Science      
> P.R. China     
> 
> 
> 
> _______________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++





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