Hello Mark--
Below is a complete scriptlet to generate and PSF and PDB, given a
(in this case bogus) sequence. Please let me know if you have
questions.
Charles
import protocol
protocol.initTopology(('protein','dihiscu'))
protocol.initParams(('protein','dihiscu'))
seq="HIS GLY GLY HIS"
import psfGen
psfGen.seqToPSF(seq)
psfGen.seqToPSF("CU2",startResid=300)
xplor.command("""
patch DIHCU2 refe=1=(resid 1) refe=2=(resid 300) refe=3=(resid 4) end
""")
protocol.genExtendedStructure()
xplor.command("write psf output=new.psf end")
protocol.writePDB("new.pdb")
On Tue, 26 Sep 2023 19:20:34 -0400,
Kelly, Mark wrote:
>
> Hello Charles,
>
> this is how I set-up my HIS/ZN-Cys patches in ARIA/CNS - how would I set-up
> and where would I put the patches for HIS-Cu-HIS (see bottom).
>
> Best,
>
> Makr
>
>
> <unambiguous_distance_restraints file="" format="ccpn" ccpn_id="23|5"
> enabled="yes" add_to_network="no" calibrate="all_iterations_except_first"
> run_network_anchoring="no" filter_contributions="yes"/>
> <ambiguous_distance_restraints file="" format="ccpn" ccpn_id="23|6"
> enabled="yes" add_to_network="no" calibrate="all_iterations_except_first"
> run_network_anchoring="no" filter_contributions="yes"/>
> <hbonds file="" format="ccpn" ccpn_id="3|11" enabled="yes"
> data_type="standard"/>
> <dihedrals file="" format="ccpn" ccpn_id="1|1" enabled="yes"
> data_type="standard"/>
> <hispatch residue="33" segid="A" proton="HISE"/>
> <znpatch type="SSSS" residue_zn="1" segid_zn="Z" residue1="25" segid1="A"
> residue2="28" segid2="A" residue3="51" segid3="A" residue4="54" segid4="A"/>
> <znpatch type="SSSE" residue_zn="1" segid_zn="Y" residue1="10" segid1="A"
> residue2="13" segid2="A" residue3="36" segid3="A" residue4="33" segid4="A"/>
> <symmetry enabled="no" method="standard" n_monomers="1"
> symmetry_type="None" ncs_enabled="no" packing_enabled="no"/>
> <initial_structure file="" format="iupac" ccpn_id="" enabled="no"/>
> </data>
> <structure_generation engine="cns”>
>
>
>
> > On Sep 1, 2023, at 3:25 PM, Charles Schwieters <[email protected]>
> > wrote:
> >
> >
> > Hello Mark--
> >
> >>
> >> we would like to calculate a structure of a protein where a Cu atom
> >> is bound to histidine residues. Can you tell us how to set-up the
> >> histidine patches for Cu? I have done this before for Zn in CNS.
> >
> > In Xplor-NIH's toppar subdirectory there is dihiscu.top/par which
> > contains a patch (and parameters) for ligating two histidines to
> > Cu(II) via the NE2 atom. This might be modified if there are a
> > different number of ligated histidines. Please let us know if you need
> > assistance with this.
> >
> > best regards--
> > Charles
>
>
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