[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
> >> Please don't post (un)subscribe requests to the list. Use the
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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 --------------
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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
>
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
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> Please don't post (un)subscribe requests to the list. Use the
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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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