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@salilab.org wrote: > Send modeller_usage mailing list submissions to > modeller_usage@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@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@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@salilab.org > Subject: Re: RE: [modeller_usage] wrong topology for > the ligand? > To: Youbin Tu ytu@mix.wvu.edu > Cc: modeller_usage@salilab.org > Message-ID: 20041118001613.GA10023@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@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@adelaide.edu.au > Subject: Re: RE: [modeller_usage] wrong topology for > the ligand? > To: modeller_usage@salilab.org > Message-ID: > 1100737894.419bed669e891@pandani.services.adelaide.edu.au > Content-Type: text/plain; charset=ISO-8859-1 > > Quoting Youbin Tu ytu@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@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 3, Issue 113 > **********************************************