[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=======
>Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
>or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
>
>You can reach the person managing the list at
> gmx-users-owner at gromacs.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of gmx-users digest..."
>
>
>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
>> www interface or send it to gmx-users-request at gromacs.org.
>>
>>
>
>--
>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 SèAerhàl
>
>
>
>------------------------------
>
>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 --------------
>An HTML attachment was scrubbed...
>URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20050420/1dbb230d/attachment-0001.htm
>
>------------------------------
>
>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...
>URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20050420/5e7890e8/attachment-0001.htm
>
>------------------------------
>
>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
More information about the gromacs.org_gmx-users
mailing list