- modeller_usage - salilab.org

chain identifiers
by John Simms 02 Dec '04

02 Dec '04

Hi All, I am generating a number of models based on soluble protein. There is a large loop in the protein which i dont wish to include in my models, but i do want to add a chain break. Is there a way for the residues in the resulting models to have different chain identifiers before and after the break? Any help would be very gratefully received John

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Re: [modeller_usage] multi domain protein help
by Mr.Sridhar 01 Dec '04

01 Dec '04

Hi Ranjit, There should be atleast a small region of overlapping structure between the consecutive domains to get the domains in their proper orientation. Make a structural alignment of the three domains, and to this profile align your sequence. Use this for modeller. Regards.

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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 29 Nov '04

29 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 29 Nov '04

29 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 29 Nov '04

29 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 29 Nov '04

29 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 18 Nov '04

18 Nov '04

Please unsuscribe

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