modeling homodimer with hetero atoms
Dear all, I am trying to model a homodimer with heteroatoms from a homodimer template. when make homodimer without heteroatoms it goes fine but when i try to build homodimer with heteroatoms it doesn't run and shows some errors regarding alignment mistakes. My template protein consists of number of Waters, and other residues. All the htatms are given at the end of A and B chains and given the chain ids according to their chains they are attached with. I have removed all waters except three (1 is atached to A and 2 with B chain). So for now I have 7 and 8 hetatm on chain A and B respectively What should be the alignment look like? I am giving 7 dots at the end of A chain and 8 dots at the end of B chain as followes:
>P1;2N0Y structureX:2N0Y:83 :A:687 :B: ferredoxin:Azotobacter vinelandii: 1.90: 0.19 -------------------------------------------PDMDTSF VGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE QGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGIPMVVFTG QVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEAFEIATS GRPGPVLVDLPKDVTAAILRNPIPTKTTLPSTSRAQDEFVMQSINKAADL INLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGLGSFDQED PKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKFAPEARRA AAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSK-----IFP VKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDTGRH VIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVAKP ESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQSLF YEHRYSHTHQLN-----PDFIKLAEAMGLKGLRVKKQEELDAKLKEFVST KG-PVLLEVEVDKKVPVLPMVAGGSGLDEFINFDPEVERQQTELRHKRTG GKH/......./-------------------------------------------PDMDTSF VGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE QGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGIPMVVFTG QVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEAFEIATS GRPGPVLVDLPKDVTAAILRNPIPTKTTLPS-SRAQDEFVMQSINKAADL INLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGLGSFDQED PKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKFAPEARRA AAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSK-----IFP VKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDTGRH VIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVAKP ESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQSLF YEHRYSHTHQLN-----PDFIKLAEAMGLKGLRVKKQEELDAKLKEFVST KG-PVLLEVEVDKKVPVLPMVAGGSGLDEFINFDPEVERQQTELRHKRTG GKH/......../*
>P1;IRSH_NT sequence:IRSH_NT:44 :A:633 :B: ferredoxin:Peptococcus aerogenes: 2.00:-1.00 MSTNETSRAIEDHTTVSAPTKPHSPTFKPEPHSAANEPKHPAARPKHVAL QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHE QGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITG QVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAAS GRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYKPNTKPHSRQ-VREAAKL IAAARKPVLYVGGGVIR-GEATEQLRELAELTGIPVVTTLMARGAFPDSH RQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAK-- -------VIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG TIEMADWWAYLNGVRKTYPLSYGPQSDGS-LSPEYVIEKLGEIA---GPD AVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALP GTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQWQSLF YAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAI NDCPVVIDFIVGADAQVWPMVAAGTSNDEI-----QAARGIRPLFDDITE GHA/......./MSTNETSRAIEDHTTVSAPTKPHSPTFKPEPHSAANEPKHPAARPKHVAL QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHE QGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITG QVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAAS GRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYKPNTKPHSRQ-VREAAKL IAAARKPVLYVGGGVIR-GEATEQLRELAELTGIPVVTTLMARGAFPDSH RQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAK-- -------VIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG TIEMADWWAYLNGVRKTYPLSYGPQSDGS-LSPEYVIEKLGEIA---GPD AVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALP GTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQWQSLF YAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAI NDCPVVIDFIVGADAQVWPMVAAGTSNDEI-----QAARGIRPLFDDITE GHA/......../*
Error that I am getting is: read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 607) Alignment .....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKH PDB ....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE Match ***** * * * Alignment residue type 13 (P, PRO) does not match pdb residue type 3 (D, ASP), for align code 1N0H (atom file 1N0H), pdb residue number "84", chain "B"
Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly.
I don't know why this error is appearing at the time of modeling with hetatm?
Please help, Regards, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand
________________________________ From: "modeller_usage-request@salilab.org" modeller_usage-request@salilab.org To: modeller_usage@salilab.org Sent: Tuesday, 1 May 2012 4:15 AM Subject: modeller_usage Digest, Vol 11, Issue 51
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Today's Topics:
1. Re: procheck problem. (Thomas Evangelidis) 2. Re: modelling with hetatms (Joel Tyndall)
----------------------------------------------------------------------
Message: 1 Date: Mon, 30 Apr 2012 14:05:39 +0300 From: Thomas Evangelidis tevang3@gmail.com To: modeller_usage@salilab.org Subject: Re: [modeller_usage] procheck problem. Message-ID: CAACvdx0LXyGWDhf0v+WGutoyXeEvpj7OD6pvNbJGXSjsgX5G3A@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Probably you overdid it with minimization. Try a smoother energy minimization scheme, e.g. 500-1000 steps. Also bare in mind that molecular mechanics force fields are not designed to produce crystallographic quality structures. I would rather use Rosetta (or PyRosetta) or http://www.yasara.org/minimizationserver.htm if I wanted to improve atom clashes, dihedral angles, secondary structure, etc.
HTH, Thomas
On 30 April 2012 13:47, vishal Nemaysh vishal.bioinfotech@gmail.com wrote:
> Respected Sir, > > I have tried to minimize my pdb structure which is modeled by Modeller9v8. > i use the Discovery Studio plateform to minimize this pdb structure by > applying CHARMm force field and applying steepest descent and after that > conjugate gradient algorithm. > but the problem here is that the procheck result is not good as earlier. > such as in Ramachandran plot 87% amino acids are in favorable region before > minimization but after minimization only 55% amino acids are in favorable > range...so plz sir suggest me some solutions.... > > Thanking you, > > Your Sincerely > > -- > Vishal > Research Scholar, > University of Delhi, > North Campus > Delhi-110007 > M: 91+9650736653 > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >
On 5/18/12 1:20 AM, NUTAN CHAUHAN wrote: > I am trying to model a homodimer with heteroatoms from a homodimer > template. when make homodimer without heteroatoms it goes fine but when > i try to build homodimer with heteroatoms it doesn't run and shows some > errors regarding alignment mistakes.
OK, so the problem is your alignment doesn't match your PDB. You just need to fix that.
> What should be the alignment look like?
The alignment looks fine, but of course you didn't attach your PDB file so there's no way to independently tell whether they match. But the Modeller error message below looks pretty clear to me:
> Alignment .....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKH > PDB ....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE > Match ***** * * *
(The formatting got a little messed up in the email, but if you look in the original log file it should be lined up properly.) You have one more '.' in your alignment file in the B chain than you have in the PDB. Either you deleted one too many HETATM residues from your PDB file, or you added one too many to your alignment file.
Ben Webb, Modeller Caretaker
Many thanx for quick response. This problem is solved..actually problem was in script..i just needed to put "env.io.water=True" to allow water as modeller was not reading water as hetatm and reading it as alignment mismatch with pdb. Its done now. thanx a lot. One more query related to this is: Is there any way to assign the residue numbers starting from 1 to each of the chain in the model? actually when I run modeller to model dimer, it assigns numbers to the residues of chain A and continues to chainB like if chain a get finished at 100 then it starts chain B from 101.
thnx in advance. regards, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand
________________________________ From: NUTAN CHAUHAN nutanbt@yahoo.co.in To: "modeller_usage@salilab.org" modeller_usage@salilab.org Sent: Friday, 18 May 2012 1:50 PM Subject: modeling homodimer with hetero atoms
Dear all, I am trying to model a homodimer with heteroatoms from a homodimer template. when make homodimer without heteroatoms it goes fine but when i try to build homodimer with heteroatoms it doesn't run and shows some errors regarding alignment mistakes. My template protein consists of number of Waters, and other residues. All the htatms are given at the end of A and B chains and given the chain ids according to their chains they are attached with. I have removed all waters except three (1 is atached to A and 2 with B chain). So for now I have 7 and 8 hetatm on chain A and B respectively What should be the alignment look like? I am giving 7 dots at the end of A chain and 8 dots at the end of B chain as followes:
>P1;2N0Y structureX:2N0Y:83 :A:687 :B: ferredoxin:Azotobacter vinelandii: 1.90: 0.19 -------------------------------------------PDMDTSF VGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE QGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGIPMVVFTG QVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEAFEIATS GRPGPVLVDLPKDVTAAILRNPIPTKTTLPSTSRAQDEFVMQSINKAADL INLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGLGSFDQED PKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKFAPEARRA AAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSK-----IFP VKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDTGRH VIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVAKP ESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQSLF YEHRYSHTHQLN-----PDFIKLAEAMGLKGLRVKKQEELDAKLKEFVST KG-PVLLEVEVDKKVPVLPMVAGGSGLDEFINFDPEVERQQTELRHKRTG GKH/......./-------------------------------------------PDMDTSF VGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE QGAGHMAEGYARASGKPGVVLVTS GPGATNVVTPMADAFADGIPMVVFTG QVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEAFEIATS GRPGPVLVDLPKDVTAAILRNPIPTKTTLPS-SRAQDEFVMQSINKAADL INLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGLGSFDQED PKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKFAPEARRA AAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSK-----IFP VKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDTGRH VIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVAKP ESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQSLF YEHRYSHTHQLN-----PDFIKLAEAMGLKGLRVKKQEELDAKLKEFVST KG-PVLLEVEVDKKVPVLPMVAGGSGLDEFINFDPEVERQQTELRHKRTG GKH/......../*
>P1;IRSH_NT sequence:IRSH_NT:44 :A:633 :B: ferredoxin:Peptococcus aerogenes: 2.00:-1.00 MSTNETSRAIEDHTTVSAPTKPHSPTFKPEPHSAANEPKHPAARPKHVAL QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHE QGAGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITG QVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAAS GRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYKPNTKPHSRQ-VREAAKL IAAARKPVLYVGGGVIR-GEATEQLRELAELTGIPVVTTLMARGAFPDSH RQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAK-- -------VIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG TIEMADWWAYLNGVRKTYPLSYGPQSDGS-LSPEYVIEKLGEIA---GPD AVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALP GTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQWQSLF YAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAI NDCPVVIDFIVGADAQVWPMVAAGTSNDEI-----QAARGIRPLFDDITE GHA/......./MSTNETSRAIEDHTTVSAPTKPHSPTFKPEPHSAANEPKHPAARPKHVAL QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHE QGAGHAASGYAHVTGRVG VCMATSGPGATNLVTPLADAQMDSIPVVAITG QVGRGLIGTDAFQEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAAS GRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYKPNTKPHSRQ-VREAAKL IAAARKPVLYVGGGVIR-GEATEQLRELAELTGIPVVTTLMARGAFPDSH RQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAK-- -------VIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG TIEMADWWAYLNGVRKTYPLSYGPQSDGS-LSPEYVIEKLGEIA---GPD AVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGLGTMGFAIPAAMGAKIALP GTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGMVRQWQSLF YAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARAI NDCPVVIDFIVGADAQVWPMVAAGTSNDEI-----QAARGIRPLFDDITE GHA/......../*
Error that I am getting is: read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 607) Alignment .....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKH PDB ....PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNFVLPKHE Match ***** * * * Alignment residue type 13 (P, PRO) does not match pdb residue type 3 (D, ASP), for align code 1N0H (atom file 1N0H), pdb residue number "84", chain "B"
Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly.
I don't know why this error is appearing at the time of modeling with hetatm?
Please help, Regards, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand
________________________________ From: "modeller_usage-request@salilab.org" modeller_usage-request@salilab.org To: modeller_usage@salilab.org Sent: Tuesday, 1 May 2012 4:15 AM Subject: modeller_usage Digest, Vol 11, Issue 51
Send modeller_usage mailing list submissions to modeller_usage@salilab.org
To subscribe or unsubscribe via the World Wide Web, visit https://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: procheck problem. (Thomas Evangelidis) 2. Re: modelling with hetatms (Joel Tyndall)
----------------------------------------------------------------------
Message: 1 Date: Mon, 30 Apr 2012 14:05:39 +0300 From: Thomas Evangelidis tevang3@gmail.com To: modeller_usage@salilab.org Subject: Re: [modeller_usage] procheck problem. Message-ID: CAACvdx0LXyGWDhf0v+WGutoyXeEvpj7OD6pvNbJGXSjsgX5G3A@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Probably you overdid it with minimization. Try a smoother energy minimization scheme, e.g. 500-1000 steps. Also bare in mind that molecular mechanics force fields are not designed to produce crystallographic quality structures. I would rather use Rosetta (or PyRosetta) or http://www.yasara.org/minimizationserver.htm if I wanted to improve atom clashes, dihedral angles, secondary structure, etc.
HTH, Thomas
On 30 April 2012 13:47, vishal Nemaysh vishal.bioinfotech@gmail.com wrote:
> Respected Sir, > > I have tried to minimize my pdb structure which is modeled by Modeller9v8. > i use the Discovery Studio plateform to minimize this pdb structure by > applying CHARMm force field and applying steepest descent and after that > conjugate gradient algorithm. > but the problem here is that the procheck result is not good as earlier. > such as in Ramachandran plot 87% amino acids are in favorable region before > minimization but after minimization only 55% amino acids are in favorable > range...so plz sir suggest me some solutions.... > > Thanking you, > > Your Sincerely > > -- > Vishal > Research Scholar, > University of Delhi, > North Campus > Delhi-110007 > M: 91+9650736653 > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >
On 5/18/12 9:28 AM, NUTAN CHAUHAN wrote: > Is there any way to assign the residue numbers starting from 1 to each > of the chain in the model?
Sure, just call rename_segments() from within automodel's special_patches() method. See http://salilab.org/modeller/9.10/manual/node28.html
Ben Webb, Modeller Caretaker
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NUTAN CHAUHAN