modeller_usage November 2004

modeller_usage@salilab.org

21 participants
24 discussions

(no subject)
by anagha＠mbu.iisc.ernet.in 28 Dec '04

28 Dec '04

dear sir, I am new to modeller user and also to linux system. i have downloaded and installed modeller But as it doent have GUI. How will I start using it. I need help. Thank you Anagha

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multi domain protein help
by Ranjit Kumar 30 Nov '04

30 Nov '04

hi i have to model a protein that has 3 domains all crystallized in different organism.i am new in modelling, can anybody help me in this regard?

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combining two proteins
by Han Choe 30 Nov '04

30 Nov '04

Dear all, Let's say that I have two pdb files of protein A and protein B and that approximate interactions of the two proteins are known. Then can I get a complex structure using MODELLER by restraining the distances of two or three interactions between A and B in the top file with the following type of alignment file? >P1;A structureX:A --AAAAA--/------------* >P1;B structureX:B -------------/--BBBBB--* >P1;AB sequence:AB --AAAAA--/--BBBBB--* Cheers, Han

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problem
by vivek sharma 30 Nov '04

30 Nov '04

Dear sir, To generate a model containing Hydrogen atoms, is it necessary that templates should have Hydrogen atoms too or these will be modeled by MODELER itself? Thanking you, sincerely, Vivek Sharma -- VIVEK SHARMA HBG BI

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Modelling multiple chains
by gerald.quon＠utoronto.ca 30 Nov '04

30 Nov '04

Hi, I'm interested in modelling a dimer composed of two chains. I would definitely like to avoid modelling each chain separately, then combining the PDB files - is it possible to model them together in MODELLER? I would try just concatenating the two chains into one, but i'm guessing the discontinuity of the backbone will mess around with the minimization... Gerald

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upper and lower distance restraints
by Youbin Tu 30 Nov '04

30 Nov '04

Hi all: I want to define some restraints in the top file. Assume we know the maximum and minimum distances between two atoms (non-bond), Which form and group type should we use? since there are so many types of groups to define distance restraints, which one should I use for my case? I looked through the manual, but did not find enough talking about it. Here is an example, The maximum distance between Fe:513 and C7:514 is 6.0(1.0) The miminum distance between Fe:513 and C7:514 is 2.0(1.0) I included the following line in the top file: SUBROUTINE ROUTINE = 'special_restraints' ADD_RESTRAINT ATOM_IDS = 'FE:513' 'C7:514', ; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 6.0 1.0 ADD_RESTRAINT ATOM_IDS = 'FE:513' 'C7:514', ; RESTRAINT_PARAMETERS = 1 1 1 21 2 2 0 2.0 1.0 RETURN END_SUBROUTINE Is it correct? Again, If I did so, does that mean that the program have to force the distance between those 2 atoms within that range even though it may take the risk to corrupt the whole structure? Or if some restraints will destroy the whole structure, the program will discard the user's restraints in order to " save" the final model? thanks. youbin ---------------------- Youbin Tu CCMM Lab,BPS Schoof of Pharmacy,WVU

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How to preserve internal coordinates for identical residues
by James T Metz 29 Nov '04

29 Nov '04

Modeller Users, Sorry if this is a FAQ, but ... Is there a simple command or set of TOP keywords that will preserve internal coordinates (especially dihedral angles) when an amino acid in my structure file and the amino acid in my alignment file are identical? In other words, I would like to constrain (fix) internal coordinates when there is no change of amino acids when building homology models. Please also comment if for some reason this is not a good idea. Regards, Jim Metz James T. Metz, Ph.D. Research Investigator Chemist GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A. Office (847) 936 - 0441 FAX (847) 935 - 0548 james.metz(a)abbott.com This communication may contain information that is legally privileged, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any dissemination, distribution, use, or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or return email and delete it from his or her computer.

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Re: RE: [modeller_usage] wrong topology for the ligand?
by Youbin Tu 19 Nov '04

19 Nov '04

Hi all: Thanks for you guys' kind help,which made me know a lot. Although I have not found out exactly which step is wrong. I figured out one way to pass by the problem. Just to output the ligand from InsightII in a pdb format, and use the pdb file as another template for the protein you want to model,of course, some restraints have been also defined to make the ligand properly located in the active site. The method worked very well, the ligand looks fine. Hope it can also save some time for people who have the same problems. Cheers. youbin Youbin Tu wrote: >Hi Alicia, Ben: > Thanks for your reply, which help me a lot. > But for my specific situation, the ligand I am trying to use is >phenacetin which did not exist in the template pdb file. Or to say, we >created it so as to make it docked in the active site by using some NMR >restraints. We expected to see some interactions between the ligand and >the active site which will make the active site show a differnt look >from what it is when no ligand is bound. > Now I was really confused, if the ligand can not have correct >connectivity, how can we expect to see the interactions between the >ligand and the enzyme? I mean how the follwong refinement steps which >is involved with minimization and molecular dynamics correctly dealt >with the ligand and the interaction between the ligand and the enzyme? > Again, why the ligand does not show correctly, you know , we build >the phenacetin in Builder module in InsightII and output it as a RTF >file, then append it to the top_heav.lib file. The molecule looks very >reasonable in InsightII, but after calculation by MODELLER , the ligand >looked weird. So, any other program can view RTF file so as to have a >check the connectivity of the ligand is reasonably good or not? Or if >the parameters are incomplete, how to make it complete? > Another question is whether does the RTF file provide enough >connectivity information for the ligand? Or is it because of the >special restraints we applied in MODELLER which make the connectivity >changed? You know,we even tried to use the ligand without any >restraints, the result still looked weird? > Basically, we just want to build a new ligand with some experimental >restraints in the active site of a enzyme. If the ligand looked werid, >we have to doubt whether the interaction between the ligand and the >enzyme is reliable or not? So, we have to know which step create this >problem? > 1. building the ligand (RFT file)? We did not give enough connectivity >information? > 2. running MODELLER? Since there is no restraints to confine the bond >or angles for the ligand or the restraints are conflicting with each >other which make the ligand broken? > 3. outputting file from MODELLER? Assumed that all the above is good, >the only problem is that MODDLER only give the cooridinates of the >atoms instead of the relationship ( connectivity) between atoms? > Hope I have well explained my problems? And I also attached my RTF >file for phenacetin. > Finally, thanks for your guys' kind help. Anyone's reply in this >topic will be highly appreciated. > Hope for the best. > > youbin > > > >Higueruelo Alicia (CAM) wrote: > > >>Hi Youbin, >> >>In my experience,(please someone correct me if I'm wrong) the ligands in >>modeller don't look great, my guess is that CHARMm deals really well >with >>aminoacids but struggle a bit with non-aminoacid atom types. (or a >least the >>version I'm using). >> >>But they look reasonable. If the ligand look really really weird. try to >>compare the "PDB atom names" in your template ( the pdb file you are >using >>to built your model) and the "PDB atom names" in your top_heavy.lib. >Hope >>the following lines are a good example. >> >>in top_heav.lib in RESI LIG "ATOM O1 OE -0.10000" >>in template.pdb "ATOM 4000 O1 LIG D 500 30.722 47.505 16.832" >> >>To have the same connection and geometry in the model-ligand than in the >>ligand-template, these PDB names should be the same "O1", I think this >is >>what is telling Modeller where to put the atom (assigning the xyz coords >>from atom called O1 from the LIG in the PDB), and "OE" is the CHARMm >atom >>type to use the potentials . >> >>In my output files, my model does not have connection data in the pdb, >>therefore the way you see you models depends which software you are >using to >>visualize your pdb, again, lots of them can not guess that a phenyl ring >>(not in a aminoacid) has alternate double bounds or aromatic bonds, and >>display them in funny ways. There are spl macros in sybyl for example, >which >>will fix some of these problems, based on the geometry of the ligands. >but >>I'm not aware of a 3D viewer which display chemically correctly all >ligands >>in pdb format. >> >>Hope this is useful, >> >>any comments on that more than welcome, >> >>cheers, >> >>alicia >> >> >>-----Original Message----- >>From: Youbin Tu [mailto:ytu@mix.wvu.edu] >>Sent: 16 November 2004 07:08 >>To: modeller_usage(a)salilab.org >>Subject: [modeller_usage] wrong topology for the ligand? >> >> >>Hi all: >> >> I am using MODELLER7V7 to build a ligand-enzyme complex, I created >>the ligand and modified the library files. Everything worked well >>except the ligand in the final result seems too weird, for example the >>benzene is not planar and there are many bonds between 2 atoms which >>should only have one bond theoritically. >> I thought maybe it is my problem when building the ligand. But >>when I tried to use GDP which already existed in the library file. The >>final >>results still have the same problem. >> Anyone knows how to deal with this kind of problem? Does it mean >>that we have to modify the par.lib or make restraints for bonds of the >>ligands? If so, can you tell me how to do that,any softwares are >>available for that purpose? >> Your reply is highly appreciated. >> >> >>youbin >> >> >> >> >> >>_______________________________________________ >>modeller_usage mailing list >>modeller_usage(a)salilab.org >>http://salilab.org/mailman/listinfo/modeller_usage >> >> >>The information contained in this email is intended for the >>personal and confidential use of the addressee only. It may >>also be privileged information. If you are not the intended >>recipient then you are hereby notified that you have received >>this document in error and that any review, distribution or >>copying of this document is strictly prohibited. If you have >>received this communication in error, please notify Celltech >>immediately on: >>+44 (0)1753 534655, or email 'is(a)celltech.co.uk' >>Celltech Group plc >>208 Bath Road, Slough, SL1 3WE, Berkshire, UK >>Registered Office as above. >> >> > >---------------------- >Youbin Tu >CCMM Lab,BPS >Schoof of Pharmacy,WVU ------------------------------------------------------------------------ Name: phn.rtf phn.rtf Type: application/msword Encoding: base64 ------------------------------------------------------------------------ _______________________________________________ >modeller_usage mailing list >modeller_usage(a)salilab.org >http://salilab.org/mailman/listinfo/modeller_usage > ---------------------- Youbin Tu CCMM Lab,BPS Schoof of Pharmacy,WVU

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(no subject)
by Leonardo René Lareo 19 Nov '04

19 Nov '04

Please unsuscribe

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restraints problem, core dumped
by Praveen Madala 18 Nov '04

18 Nov '04

Hi, I am trying to model a protein with a restrain file MODELLER6v2 VERSION: USER FORMAT R 3 1 1 21 2 2 0 7.1000 0.3387 SG:140 SG:222 R 3 1 1 21 2 2 0 15.0000 0.3387 CA:139 CA:250 R 3 1 1 22 2 2 0 17.0000 0.3387 CA:139 CA:250 R 3 1 1 21 2 2 0 15.3000 0.3387 CB:139 CB:250 R 3 1 1 22 2 2 0 17.3000 0.3387 CB:139 CB:250 R 3 1 1 21 2 2 0 10.0000 0.3387 CA:117 CA:292 R 3 1 1 21 2 2 0 6.00000 0.3387 N:117 N:292 R 3 1 1 27 2 2 0 8.00000 0.3387 CB:117 CG:208 R 3 1 1 27 2 2 0 10.0000 0.3387 CB:117 CG:208 R 3 1 1 27 2 2 0 8.00000 0.3387 CB:117 CG:211 R 3 1 1 27 2 2 0 10.0000 0.3387 CB:117 CG:211 as I mensioed before, the program is not identifying the the SG:140 CG:211, I think it is not identifying gama atoms......I dont know that how i am writing the gamma atom is wrong ??? If i removed these lines from the restrain file, the program is getting core dumped. can you please help me out this problem. Thanking you regards, Praveen On Wed, 17 Nov 2004 16:32:54 -0800 modeller_usage-request(a)salilab.org wrote: > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, >visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body >'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is >more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: RE: [modeller_usage] wrong topology for the >ligand? > (Modeller Caretaker) > 2. Re: RE: [modeller_usage] wrong topology for the >ligand? > (Cvetan Stojkoski) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 17 Nov 2004 16:16:13 -0800 >From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: RE: [modeller_usage] wrong topology for > the ligand? > To: Youbin Tu <ytu(a)mix.wvu.edu> > Cc: modeller_usage(a)salilab.org > Message-ID: <20041118001613.GA10023(a)salilab.org> > Content-Type: text/plain; charset=us-ascii > > On Wed, Nov 17, 2004 at 05:25:09AM -0500, Youbin Tu >wrote: >> Thanks for your reply, which help me a lot. >> But for my specific situation, the ligand I am trying >>to use is >> phenacetin which did not exist in the template pdb >>file. Or to say, we >> created it so as to make it docked in the active site by >>using some NMR >> restraints. We expected to see some interactions between >>the ligand and >> the active site which will make the active site show a >>differnt look >> from what it is when no ligand is bound. > > Yes - if there is no template, you will have to define >parameters for > the ligand. > >> Now I was really confused, if the ligand can not have >>correct >> connectivity, how can we expect to see the interactions >>between the >> ligand and the enzyme? > > You misunderstand me. Modeller knows the connectivity - >it reads it from > the topology file - but it doesn't write it to the final >model PDB file, > so your PDB viewer cannot read the connectivity. > >> Again, why the ligand does not show correctly, you >>know , we build >> the phenacetin in Builder module in InsightII and >>output it as a RTF >> file, then append it to the top_heav.lib file. > > The RTF file only defines the topology. It doesn't >define the > parameters. These need to be put into par.lib. This is >the case for any > molecular mechanics package, not just Modeller. > >> Another question is whether does the RTF file provide >>enough >> connectivity information for the ligand? > > Certainly. All connectivity for the ligand is included >in the RTF > (residue topology file) but you need the parameters as >well. If > InsightII has parameters defined for your ligand, you >will need to save > them as well, and put them into Modeller's par.lib file. > > Note that the topology only defines bonding >interactions, i.e. covalent > bonds within the ligand or protein. Interactions between >the ligand and > the protein are non-bonding, and are not described here >- you'd use VDW > or electrostatic interactions for that. > >> Or is it because of the special restraints we applied in >>MODELLER which >> make the connectivity changed? > > They won't change your topology, but of course, if you >have a bond > interaction which clashes with a user restraint, >Modeller will try to > compromise. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org > http://www.salilab.org/modeller/ > Modeller mailing list: >http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 2 > Date: Thu, 18 Nov 2004 11:01:34 +1030 >From: Cvetan Stojkoski <cvetan.stojkoski(a)adelaide.edu.au> > Subject: Re: RE: [modeller_usage] wrong topology for > the ligand? > To: modeller_usage(a)salilab.org > Message-ID: > <1100737894.419bed669e891(a)pandani.services.adelaide.edu.au> > Content-Type: text/plain; charset=ISO-8859-1 > > Quoting Youbin Tu <ytu(a)mix.wvu.edu>: > >> Hi Alicia, Ben: >> Thanks for your reply, which help me a lot. >> But for my specific situation, the ligand I am trying >>to use is >> phenacetin which did not exist in the template pdb >>file. Or to say, we >> created it so as to make it docked in the active site by >>using some NMR >> restraints. We expected to see some interactions between >>the ligand and >> the active site which will make the active site show a >>differnt look >> from what it is when no ligand is bound. > > You have used NMR perturbation data to dock a ligand >into the active site? You > could simulate a ligand-induced conformational change in >the receptor just by > doing some MD on your complex. I recommend NAMD. >However, AMBER will probably > work better for you since your compound has an aromatic >ring. > >> Now I was really confused, if the ligand can not have >>correct >> connectivity, how can we expect to see the interactions >>between the >> ligand and the enzyme? I mean how the follwong >>refinement steps which >> is involved with minimization and molecular dynamics >>correctly dealt >> with the ligand and the interaction between the ligand >>and the enzyme? > > MD packages rely on complete topology/parameter sets. >You can use XPLO2D to > predict a lot of this information. However, be aware >that the values are > completely derived from the pdb file and will need to be >edited. Charges will > also need to be added. > >> Again, why the ligand does not show correctly, you >>know , we build >> the phenacetin in Builder module in InsightII and >>output it as a RTF >> file, then append it to the top_heav.lib file. The >>molecule looks very >> reasonable in InsightII, but after calculation by >>MODELLER , the ligand >> looked weird. So, any other program can view RTF file so >>as to have a >> check the connectivity of the ligand is reasonably good >>or not? Or if >> the parameters are incomplete, how to make it complete? > > Although we have InsightII, I have never built an RTF >file with it. I'm guessing > it works similar to XPLO2D. Therefore you will most >certainly have to edit angle > and charge terms. However, you'd think that bonding >would be correct. > >> Another question is whether does the RTF file provide >>enough >> connectivity information for the ligand? Or is it >>because of the >> special restraints we applied in MODELLER which make >>the connectivity >> changed? You know,we even tried to use the ligand >>without any >> restraints, the result still looked weird? > > To check if your RTF file provides correct connectivity, >pass it through X-PLOR > along with your pdb file to produce a psf. You can then >view your psf file in > VMD to make sure your connectivities are correct. >Otherwise just go through the > topology manualy. > >> Basically, we just want to build a new ligand with >>some experimental >> restraints in the active site of a enzyme. If the ligand >>looked werid, >> we have to doubt whether the interaction between the >>ligand and the >> enzyme is reliable or not? So, we have to know which >>step create this >> problem? > > If you already have the structure of the protein you are >docking to then I > wouldn't recommend using MODELLER to dock your ligand >and observe ligand-induced > confomrational changes. Do MD. > >> 1. building the ligand (RFT file)? We did not give >>enough connectivity >> information? >> 2. running MODELLER? Since there is no restraints to >>confine the bond >> or angles for the ligand or the restraints are >>conflicting with each >> other which make the ligand broken? >> 3. outputting file from MODELLER? Assumed that all the >>above is good, >> the only problem is that MODDLER only give the >>cooridinates of the >> atoms instead of the relationship ( connectivity) >>between atoms? >> Hope I have well explained my problems? And I also >>attached my RTF >> file for phenacetin. >> Finally, thanks for your guys' kind help. Anyone's >>reply in this >> topic will be highly appreciated. >> Hope for the best. >> >> >> youbin >> > > Sorry I didn't go through your RTF file but its >laborious work even with the > smallest of compounds. Best create the psf file and then >visualize it in VMD. > > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 3, Issue 113 > **********************************************

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modeller_usage November 2004