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

Zhenting Gao zhentg at 163.com
Mon Apr 25 02:47:09 CEST 2005


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? 



======= 2005-04-21, 11:12:56 2005-04-21, 11:12:56 you wrote£º=======      

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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 
>>> 
>>> 
>>> 
>>> _______________________________________________ 
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>> 
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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 SèAerhàl 
> 
> 
> 
>------------------------------ 
> 
>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 
> 
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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 
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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 
> 
> 
> 
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> 
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= = = = = = = = = = = = = = = = = = = =      
¡¡¡¡¡¡¡¡¡¡      
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡      

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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