Hi Brian,
Have you tried to use any spectra in your calculations? Or only restraints.
Thanks.
Kind regards
Teresa Almeida
PhD student
Department of Chemistry/Institute of Integrative Biology
University of Liverpool
Liverpool
L69 7ZD
United Kingdom
________________________________________
From: CcpNmr software mailing list [[log in to unmask]] on behalf of Brian Smith [[log in to unmask]]
Sent: 30 March 2015 09:57
To: [log in to unmask]
Subject: Re: small molecule - ARIA/CCPN error
I'm pretty sure that ARIA without some modification will not calculate structures including your small molecule. Below lists the changes I had to make for adding oleic acid to a structure calculation. I ran these calculations using restraint lists generated in analysis (direct, not exported as .tbl) rather than getting ARIA to make the assignments.
One further note: When generating the starting coordinates, ARIA uses a multiple of the residue number as the x coordinate to produce an initial linear structure. If your small molecule has a residue number significantly different from your protein residues, it will end up a long way away, and the minimization may fail to bring them together.
---
Adding oleic acid ligand to structure calcs with aria 2.3.1
First copy and modify topallhdg5.3.pro and topallhdg5.3.pro to include topology and parameter definitions for ligand and ligand specific atoms, angles, dihedrals, impropers (and nonbonded if you need to - good luck!) etc. If there's an existing PDB entry then XPLO2D is a help for starting and testing the parameter and topology work. ACPYPE should be good for this also.
For the residue linking to work nicely, it seems best to leave the method on Automatic. Copy and modify ions.link to include something like
link DUMM head - OLA tail + OLA end
first DUMM tail + OLA end
last DUMM head - OLA end
once you have run aria -s <project.xml> copy your modified ions.link to run1/cns/toppar overwriting the default copy. Note that you will have to repeat this copying each time you set up the project. This method is also not very elegant because it uses an undefined patch that generates errors in generate.out
%PATCH-ERR: patch DUMM not found in topology file
%PATCH-ERR: patch DUMM not found in topology file
Add a definition of the new molecule in ARIA's atomnames.xml file - you'll find this at $ARIA2/src/py/data/atomnames.xml and there should be no problem with editing the copy in the ARIA installation directory (so long as you have write permission). In fact, as this file is not copied to the working directory, you have to do it this way. For oleate something like the following seems to work
<residue residue_type="NONBASE" iupac_name="OLA" cns_name="OLA" dyana_name="OLA">
<atom iupac_name="C1" cns_name="C1" dyana_name="C1"/>
<atom iupac_name="C2" cns_name="C2" dyana_name="C2"/>
<atom iupac_name="C3" cns_name="C3" dyana_name="C3"/>
<atom iupac_name="C4" cns_name="C4" dyana_name="C4"/>
<atom iupac_name="C5" cns_name="C5" dyana_name="C5"/>
<atom iupac_name="C6" cns_name="C6" dyana_name="C6"/>
<atom iupac_name="C7" cns_name="C7" dyana_name="C7"/>
<atom iupac_name="C8" cns_name="C8" dyana_name="C8"/>
<atom iupac_name="C9" cns_name="C9" dyana_name="C9"/>
<atom iupac_name="C10" cns_name="C10" dyana_name="C10"/>
<atom iupac_name="C11" cns_name="C11" dyana_name="C11"/>
<atom iupac_name="C12" cns_name="C12" dyana_name="C12"/>
<atom iupac_name="C13" cns_name="C13" dyana_name="C13"/>
<atom iupac_name="C14" cns_name="C14" dyana_name="C14"/>
<atom iupac_name="C15" cns_name="C15" dyana_name="C15"/>
<atom iupac_name="C16" cns_name="C16" dyana_name="C16"/>
<atom iupac_name="C17" cns_name="C17" dyana_name="C17"/>
<atom iupac_name="C18" cns_name="C18" dyana_name="C18"/>
<atom iupac_name="H1" cns_name="H1" dyana_name="H1"/>
<atom iupac_name="H21" cns_name="H21" dyana_name="H21"/>
<atom iupac_name="H22" cns_name="H22" dyana_name="H22"/>
<atom iupac_name="H31" cns_name="H31" dyana_name="H31"/>
<atom iupac_name="H32" cns_name="H32" dyana_name="H32"/>
<atom iupac_name="H41" cns_name="H41" dyana_name="H41"/>
<atom iupac_name="H42" cns_name="H42" dyana_name="H42"/>
<atom iupac_name="H51" cns_name="H51" dyana_name="H51"/>
<atom iupac_name="H52" cns_name="H52" dyana_name="H52"/>
<atom iupac_name="H61" cns_name="H61" dyana_name="H61"/>
<atom iupac_name="H62" cns_name="H62" dyana_name="H62"/>
<atom iupac_name="H71" cns_name="H71" dyana_name="H71"/>
<atom iupac_name="H72" cns_name="H72" dyana_name="H72"/>
<atom iupac_name="H81" cns_name="H81" dyana_name="H81"/>
<atom iupac_name="H82" cns_name="H82" dyana_name="H82"/>
<atom iupac_name="H9" cns_name="H9" dyana_name="H9"/>
<atom iupac_name="H10" cns_name="H10" dyana_name="H10"/>
<atom iupac_name="H111" cns_name="H111" dyana_name="H111"/>
<atom iupac_name="H112" cns_name="H112" dyana_name="H112"/>
<atom iupac_name="H121" cns_name="H121" dyana_name="H121"/>
<atom iupac_name="H122" cns_name="H122" dyana_name="H122"/>
<atom iupac_name="H131" cns_name="H131" dyana_name="H131"/>
<atom iupac_name="H132" cns_name="H132" dyana_name="H132"/>
<atom iupac_name="H141" cns_name="H141" dyana_name="H141"/>
<atom iupac_name="H142" cns_name="H142" dyana_name="H142"/>
<atom iupac_name="H151" cns_name="H151" dyana_name="H151"/>
<atom iupac_name="H152" cns_name="H152" dyana_name="H152"/>
<atom iupac_name="H161" cns_name="H161" dyana_name="H161"/>
<atom iupac_name="H162" cns_name="H162" dyana_name="H162"/>
<atom iupac_name="H171" cns_name="H172" dyana_name="H172"/>
<atom iupac_name="H172" cns_name="H172" dyana_name="H172"/>
<atom iupac_name="H181" cns_name="H181" dyana_name="H181"/>
<atom iupac_name="H182" cns_name="H182" dyana_name="H182"/>
<atom iupac_name="H183" cns_name="H183" dyana_name="H183"/>
<atom iupac_name="O1" cns_name="O1" dyana_name="O1"/>
<atom iupac_name="O2" cns_name="O2" dyana_name="O2"/>
</residue>
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089
----------------------------------------------------------------------
The University of Glasgow, charity number SC004401
________________________________________
From: CcpNmr software mailing list [[log in to unmask]] on behalf of Barsukov, Igor [[log in to unmask]]
Sent: 28 March 2015 14:43
To: [log in to unmask]
Subject: Re: small molecule - ARIA/CCPN error
Hello,
This non-standard molecule is classified as "other" and lacks code3Letter that is used to for the residue name when generating Aria chains from CCPN project. This explains the missing residue name in the PDB file. Is there a way to set code3Letter for non-standard molecules in the project? Or should a different attribute be used for small molecules when generating the chain?
And a related question, would missing code3Letter create a problem when extracting peaks and shift lists from the CCPN project and converting them to Aria format? This is the second error message below.
Thanks
Igor
Dr. Igor Barsukov
University of Liverpool,
Institute of Integrative Biology,
Biosciences Building,
Crown Street,
Liverpool L69 7ZB
Tel: +44 151 795 4307
________________________________________
From: CcpNmr software mailing list [[log in to unmask]] on behalf of Almeida, Teresa [[log in to unmask]]
Sent: 27 March 2015 17:16
To: [log in to unmask]
Subject: small molecule - ARIA/CCPN error
Hi,
I have a complex between a protein and a small molecule that I would like to use for a structure calculation in ARIA.
The problem is if I try it straight from CCPN into ARIA, the PDB in the directory run1/cns/data/sequence doesn't have residue name for the small molecule - file attached. I made sure the molecule name in CCPN is a three letter code as a residue would have (in case this was the problem).
The traceback is
------------------------------------------------
Traceback (most recent call last):
File "/usr/local/prog/aria_cns/aria2.3/aria2.py", line 903, in <module>
verbose_level, use_condor=condor)
File "/usr/local/prog/aria_cns/aria2.3/aria2.py", line 813, in run_aria
project.go(use_condor)
File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/Project.py", line 1573, in go
first_iteration = self.finalize()
File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/Project.py", line 1558, in finalize
protocol.finalize_engine(self.getMolecule())
File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/Protocol.py", line 1525, in finalize_engine
engine.prepare(self.getSettings(), molecule)
File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/cns.py", line 1958, in prepare
self.generate_template_pdb(protocol_settings, replace)
File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/cns.py", line 1910, in generate_template_pdb
self.error(IOError, s)
File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/ariabase.py", line 211, in error
raise exception, msg
IOError: USER ERROR <aria.cns.CNS> File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/cns.py", line 1958 in prepare
Creation of template PDB-file was not successful.
-----------------------------------------------
If I create the this PDB file myself I get, the following error:
---------------------------------------------------------------------
WARNING [Project]: More than 90% of the cross peaks could not be assigned. This
might be due to interchanged frequency dimensions or
undersized frequency windows. Please check your setup.
--------------------------------------------------------------------
It doesn't seem to recognize any of the assigned peaks belonging to my small molecule.
The only way I managed to get my calculations to work is by creating pdb file manually and convert all the restraints in .tbl files and not using any spectra at all. It doesn't work if I use restraints from CCPN.
Is there an easier way of doing it, where I could use ARIA to extract information of the small molecule from CCPN as one would usually do for proteins?
Thanks in advance.
Kind regards
Teresa Almeida
PhD student
Department of Chemistry/Institute of Integrative Biology
University of Liverpool
Liverpool
L69 7ZD
United Kingdom
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