I am trying to build a protein-ligand model using align-ligand.ali file. . Below is the python script to generate 5 model and to calculate the Dope and GA score. but I am unable to calculate the DOPE score and GA score. Plz help
from modeller import *
from modeller.automodel import *
log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in
Message: 1 Date: Mon, 09 Apr 2012 11:46:02 -0700 From: Modeller Caretaker <" href="mailto:">> To: BIN ZHANG <" href="mailto:">> Cc:
" href="mailto:"> Subject: Re: [modeller_usage] In what are the initial structures different? Message-ID: <" href="mailto:">> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 04/08/2012 11:58 PM, BIN ZHANG wrote: > I have a question about the differences of the initial structure built > for homology modeling. Can anyone tell me how exactly are these initial > structures different? Do they differ in the secondary structures in > uncertain regions? I cannot find this information in the manual.
Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file. So it could probably be '2AHNA' or '2AHNB'.
Message: 2 Date: Mon, 9 Apr 2012 17:21:12 +0530 From: Sumedha Roy <" href="mailto:">> To: modeller usage <" href="mailto:">> Subject: [modeller_usage] Error in ALIGN_CODES(i) Message-ID: <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=" href="mailto:">> Content-Type: text/plain; charset="iso-8859-1"
Hello all,
When I try to model my protein-DNA complex, I get the error: _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = 2AHN
But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!!
On 04/09/2012 04:51 AM, Sumedha Roy wrote: > When I try to model my protein-DNA complex, I get the error: > _modeller.ModellerError: read_al_373E> Protein specified in > ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( > 2) = 2AHN > > But I see no mistake either in the alignment or the format. I've > attached both the ALI file and model-ligand.py. Please help!!!
Your alignment file is in incorrect format. Each sequence must start with a >P1; header. Your second sequence starts with >P2; instead.
Dear BIN ZHANG, MODELLER based on your constructed alignment file parsing the reliable template residues mapped against the target ones, constructs and fixes the average alpha carbon backbone (if you choose a single template) or an average backbone topology (for Multiple templates' local aligned chunks). Then it fits in the side chains and backbone atoms to make the model complete.
However, easy saying but really a vicious circle problem, the alignment could have actually been wrong to incorrectly fit target against parsed template residues. Regardless of the earlier problems, On increased sampling, MODELLER tries best to satisfy the Lennard Jones and all the energetic equations composing its DOPE energy function. The non-physical local atomic clashes are thus minimized with every such iteration. So only you see, Restraints earlier, now with end of every such iterative step. That in fact, is the trial to leap the energetic landscape, precisely focusing on the probably erroneous regions encompassing the higher local steric clashes.
The story continues until the number of iterations are over.
Message: 1 Date: Sun, 8 Apr 2012 23:58:13 -0700 From: BIN ZHANG
<" href="mailto:">> To: " href="mailto:"> Subject: [modeller_usage] In what are the initial structures different? Message-ID: <" href="mailto:">> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Dear All:
I have a question about the differences of the initial structure built for homology modeling. Can anyone tell me how exactly are these initial structures different? Do they differ in the secondary structures in uncertain regions? I cannot find this information in the manual.
For example, by
using
a = automodel() a.starting_model = 1 a.ending_model = 50
I can built 50 different homology models starting from different initial structures, but I have want to know how these different initial structures are constructed.