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best but ACPYPE websites are outdated and don't support antichamber18).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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