I'm trying to do a loop refinement calculation with the
dopehr_loopmodelclass, modeller 9v4.
Here's the python script I'm using:
from modeller import *
from modeller.automodel import *
log.verbose() # request verbose output
env = environ()
# directories for input atom files
env.io.atom_files_directory = ['./', 'PDB/']
a = dopehr_loopmodel(env,
alnfile='TTN.ali',
knowns='2g8gOligo',
sequence='1s58',
assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 1
a.md_level = None # No refinement of model
a.loop.starting_model = 1
a.loop.ending_model = 1
a.loop.md_level = refine.fast
a.make()
After a few hours of running, it stop. Here's the last part of the log:
...
randomi_498_> Atoms,selected atoms,random_seed,amplitude: 36972
36056 1 5.0000
randomi_496_> Amplitude is > 0; randomization is done.
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 327553569
319876.531 312.379
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 554709537
541708.562 529.012
preppdf_458W> Both Lennard-Jones and statistical potential terms selected.
check_inf__E> Atom 31754 has out-of-range coordinates (usually infinity).
The objective function can thus not be calculated.
>> Summary of successfully produced models:
Filename molpdf DOPE score GA341 score
----------------------------------------------------------------------
1s58.B99990001.pdb 75059.09375 -361379.46875 0.78559
>> Summary of failed loop models:
1s58.BL00010001.pdb check_inf__E> Atom 31754 has out-of-range
coordinates (usually infinity).
The objective function can thus not be calculated.
Dynamically allocated memory at finish [B,KiB,MiB]: 549216697
536344.438 523.774
Starting time : 2008/10/24
10:37:24
Closing time : 2008/10/24
12:51:48
Total CPU time [seconds] : 8018.72
The model part went OK, but when it tried to do the loop refinement it went
crazy (the coordinates in1s58.BL00010001.pdb are all messed up).
I'm also testing the other two classes (loopmodel and dope_loopmodel) and
they've been running for a long while now, so I don't know if they'll work
or not. I'd just like to
know if I'm doing something wrong or I just ran into some kind of glitch or
bug in the dopehr algorithm.
Thanks!
--
0 | Mauricio Carrillo Tripp, PhD
/ | Department of Molecular Biology, TPC6
0 | The Scripps Research Institute
\ | 10550 North Torrey Pines Road
0 | La Jolla, California 92037
/ | trippm(a)scripps.edu
0 | http://www.scripps.edu/~trippm
** Aut tace aut loquere meliora silentio **
Dear Alden,
Thank you for your reply and your information. My idea is very
similar to the idea presented in this nice paper. But the the
approaches they used are beyond the limit of my knowledge. I hope
some one can implement their results into a public available program
(for example, Modeller, PyMol or Deep Viewer).
Direct homology modeling of phosphorylated polypeptide may not make
any sense if the template used is not phosphorylated because the
conformational change. But if a molecular modeling program allows to
add the phosphate group on a model (similar to adding S-S bridge in
Modeller) followed by MD simulation, the final model could make sense
(Groban et al's paper is very encouraging).
I noticed that in the topological library of Modeller9v4, there are
information for "converting (patching?) tyrosine to monoanionic
phosphotyrosine (PRES TP1)", but no information on converting Thr,
Ser and Asp. I wonder if any body tried to patch a model from
Tyrosine to phosphotyrosine with Modeller. Is there any possibility
to implement information for other residues for patching purpose?
Is there any other free program which has this functionality?
Thank you for your comments and suggestions.
Best regards,
Xiao-Ping
At 02:16 AM 10/29/2008, you wrote:
>Perhaps homology modelling is not the best method. This might help:
>
>http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1440919
>
>Best of luck.
>
>~alden
>
>
>Xiao-Ping Zhang wrote:
> > Hi,
> >
> > Many proteins are phosphorylated in vivo and and the status of their
> > phosphorylation correlate to their function. The residues which are
> > phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry.
> > I wonder how to build a phosphorylated model directly or how to apply a
> > patch on a model to get a phosphorylated model in Modeller?
> >
> > Thank you advance for your suggestions.
> >
> > Xiao-Ping Zhang
> >
> >
> >
> > _______________________________________________
> > modeller_usage mailing list
> > modeller_usage(a)salilab.org
> > https://salilab.org/mailman/listinfo/modeller_usage
> >
> >
Hi,
Many proteins are phosphorylated in vivo and and the status of their
phosphorylation correlate to their function. The residues which are
phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry.
I wonder how to build a phosphorylated model directly or how to apply a
patch on a model to get a phosphorylated model in Modeller?
Thank you advance for your suggestions.
Xiao-Ping Zhang
Hi, All:
I was trying to add missing residues in pdb file according to the page:
http://salilab.org/modeller/wiki/Missing%20residues
But, one thing I don't understand is how can I get the "alignment.ali"
file?
Aslo, it seems to me the command complete_pdb() can also do the job?
http://salilab.org/modeller/manual/node403.html
Is this true? If so, what's the difference between these 2?
Thanks a lot.
Bin
-------------------------------------------------------------
The tree of liberty must be refreshed from time to time with the blood
of patriots and tyrants.
When I run the automodel or the loopmodel classes, either way I get a
target.B99990001.pdb for the
structure of the final model. From the documentation, I understand that in
the case of the loopmodel, an
extra pdb file will be produced with refined loops.
My question is:
Should the models in files target.B99990001.pdb be the same whether I use
automodel or loopmodel?
(provided I'm using the same optimizations and all, I'm just changing the
class name in the python script)
Thanks!
--
0 | Mauricio Carrillo Tripp, PhD
/ | Department of Molecular Biology, TPC6
0 | The Scripps Research Institute
\ | 10550 North Torrey Pines Road
0 | La Jolla, California 92037
/ | trippm(a)scripps.edu
0 | http://www.scripps.edu/~trippm
** Aut tace aut loquere meliora silentio **
Dear users,
There is a PATCH for adding sulfide bridge among two sulfur atom in a
peptide.Can we use this concept for adding two residues of two different
peptides at a certain angle...........
please give me some suggestions
thanx in advance
--
PRASUN (ASHOKA)
Dear users,
I am trying to add two proteins by means of making bond between the residues
of both the proteins.Can we do this using modeller.
this question came into my mind because of the DISULFIDE bond that we can
make using modeller.
if there is any method then please help me
thanx in advance
--
PRASUN (ASHOKA)
Hi,
I'm new in Modeller (9v4) and I haven't been able to find an
answer to the following question anywhere I've looked:
Is there a way to keep the original target's residue numbering in
the final model instead of having them sequentially numbered
starting at 1?
As an example, this is my target's sequence (NOTE: "-" are not
gaps, are missing/unknown residues):
>P1;1s58
SEQUENCE:1s58.ali : 19 :A: 554 :A:::0.00:0.00
------------------NPVKSMWSEGATFSANSVTCTFSRQFLIPYDP
EHHYKVFSPAASSCHNASGKEAKVCTITPIMGYSTPWRYLDFNALNLFFS
PLEFQHLIENYGSIAPDALTVTISEIAVKDVTDKTGGGVQVTDSATGRLC
MLVDHEYKYPYVLGQGQDTLAPELPIWVYFPPQYAYLTVGDVNTQGISGD
SKKLASEESAFYVLEHSSFQLLGTGGTATMSYKFPPVPPENLEGCSQHFY
EMYNPLYGSRLGVPDTLGGDPKFRSLTHEDHAIQPQNFMPGPLVNSVSTK
-------------TGLSTGTSQNTRISLRPGPVSQPYHHWDTDKYVTGIN
AISHGQTTYGNAEDKEYQQGVGRFPNEKEQLKQLQGLNMHTYFPNKGTQQ
YTDQIERPLMVGSVWNRRALHYESQLWSKIPNLDDSFKTQFAALGGWGLH
QPPPQIFLKILPQSGPIGGIKSMGITTLVQYAVGIMTVTMTFKLGPRKAT
GRWNPQPGVYPPHAAGHLPYVLYDPTATDAKQHHRHGYEKPEELWTAKSR
VHPL
*
The final model's PDB starts with residue number 1 and ends
with residue number 523 (number of residues in the sequence).
What I would like to get is a model's PDB starting at residue
19, jumping from residue 300 to residue 314 and so, ending at
residue 554.
Thanks in advance for any pointers!
--
0 | Mauricio Carrillo Tripp, PhD
/ | Department of Molecular Biology, TPC6
0 | The Scripps Research Institute
\ | 10550 North Torrey Pines Road
0 | La Jolla, California 92037
/ | trippm(a)scripps.edu
0 | http://www.scripps.edu/~trippm
** Aut tace aut loquere meliora silentio **
Hi,
I am new to modeller. I am using mod9v4. I have quite few doubts. I performed homology modeling of particular protein , done all steps and got a model. But i have to know, how to build ions in my model??
Thanks
Best Regards
vidhya
Hi,
I want to ask that when modeller directory (Work Station) is changed from
C directory (default) than how path of atom files is changed?
I want to know the whole procedure of changing directories and giving the
right path for atom files.
Thanks,
Khramsb