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Subject:

Re: Aria2 cannot assign ligand peaks

From:

Vanessa Granitzka <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Tue, 28 May 2019 11:19:26 +0200

Content-Type:

text/plain

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text/plain (88 lines)

Hi all,

thanks to everyone for your support!
This is how we finally managed to run protein-ligand structure 
calculations on ARIA2.3.1:

we took the parameters for the ligand from PRODRG (we know it's not the 
best but ACPYPE websites are outdated and don't support antichamber18). 
Keep in mind to upload the PRODRG created .pdb file with all hydrogen to 
CCPNMR small molecules to make sure atom names are identical.

Add parameters in :	topallhdg5.3.pro (masses/charges/residues)
			mass xx etc.; 4-letter atom type
			parallhdg5.3.pro (angles etc.)

			eval ($pd_v=$pd_x*   963.6) ANGLE OM25 CM24 OM26 $pd_v 126.000
			eval ($pd_v=$pd_x*   963.9) ANGLE OM25 CM24 CM23 $pd_v 117.000

			ARIA:
  			ANGLe  C    CH1E CH1E     500.00 {sd=     0.031}    109.0754
  			ANGLe  C    CH1E CH2E     500.00 {sd=     0.031}    110.1094

			we decided to set force constants to 500.00 and standard deviation to 
0.031
  			ANGLe OM25 CM24 OM26 500.0 {sd=    0.031}   126.000
  			ANGLe OM25 CM24 CM23 500.0 {sd=    0.031}   117.000

			dihedrals: we keep multiplicity, but change force constants to 2.0 as 
used by ARIA
			 DIHEDRAL CM22 CM23 CM24 OM25 2.00      6   0.000
			 DIHEDRAL CM20 CM22 CM23 CM24 2.00      3   0.000

			nonbonded parameters (most likely wrong) added after
			 else {standard PARALLHDG parameters}
			NONBonded OM25  0.10000 2.58361 0.10000 2.31634
			NONBonded CM24  0.10000 3.29633 0.10000 3.02906

include new atom types to atomnames.xml file from PRODRG .pdb file
  <residue residue_type="NOBASE" iupac_name="CHA" cns_name="CHA" 
dyana_name="CHA">
     <atom iupac_name="O25" cns_name="O25" dyana_name="O25"/>
     <atom iupac_name="C24" cns_name="C24" dyana_name="C24"/>
     <atom iupac_name="O26" cns_name="O26" dyana_name="O26"/>

add 3-letter-code of the ligand in your CCPNMR project folder at 
/ccp/molecule/ChemComp
<CHEM.NonStdChemComp _ID="_1" ccpCode="ChA" createdBy="bionmr" 
code3Letter="CHA" 
guid="190516_MIA2_ChA_bionmr_2019-05-16-06-28-53-444_00001" 
hasStdChirality="false" molType="other">
   <CHEM.ChemComp.name>

to link intermolecular NOEs we create a .tbl file of either a new 
peaklist with only intermolecular assignments or the used protein-ligand 
peaklist - both works. therefore, we make new distance restraints using 
the peaklist of interest by klicking on make assigned restraints. we 
merge 15N and 13C lists and export as ARIA list. you'll be asked whether 
or not you want to export SEGIDs, in our case only without works. in 
ARIA we use the created .tbl file as unambiguous distances and keep the 
spectra as usual.

modify ions.link file with ligand (we call it 'CHA')
  link  DUMM head - CHA tail + CHA end
  first DUMM           tail + CHA end
  last  DUMM head - CHA           end

-> replace run1/cns/toppar generated ions.link file with modified after 
run aria2 -s xx.xml, then continue with aria2 xx.xml


Cheers,
Vanessa

-- 
Vanessa Granitzka, M.Sc.
Biomolecular NMR-Spectroscopy
NC 5/173
Faculty of Chemistry and Biochemistry
Ruhr-University Bochum
Universitaetsstr. 150
D-44801 Bochum
Tel.: +49 234 32-26246

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