MantisBT - Rosetta
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0000151Rosetta[All Projects] Incorrect Resultspublic2012-11-08 09:312017-08-07 19:56
smlewis 
amw579 
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0000151: disulfide energy terms do not handle D-cysteine
The D-cysteine parameters file DCYD.params is set up like CYD.params for disulfide bonding. However, the disulfide energy term explicitly checks for "aa_cys" in the aa enum; DCYD is aa_unk (because it uses a different set of rotamers, I believe).

These bits of code are certainly at fault:
rosetta_source/src/core/scoring/disulfides> ack-grep aa_cys
DisulfideMatchingEnergyContainer.cc
560: if ( res.aa() == chemical::aa_cys &&
622: if ( res.aa() != chemical::aa_cys ||
632: } else if ( pose.residue( ii ).aa() == chemical::aa_cys &&

CentroidDisulfideEnergyContainer.cc
566: if ( res.aa() == chemical::aa_cys &&
618: if ( res.aa() != chemical::aa_cys ||
628: } else if ( pose.residue( ii ).aa() == chemical::aa_cys &&

FullatomDisulfideEnergy.cc
184: return res_moving_wrt_eachother && res1.aa() == aa_cys && res2.aa() == aa_cys &&
440: if ( rsd1.aa() != chemical::aa_cys || rsd2.aa() != chemical::aa_cys ) return;

FullatomDisulfideEnergyContainer.cc
566: if ( pose.residue( ii ).aa() == chemical::aa_cys &&
615: if ( pose.residue( ii ).aa() != chemical::aa_cys ||
625: } else if ( pose.residue( ii ).aa() == chemical::aa_cys &&

DisulfideMatchingEnergy.cc
124: if ( rsd1.aa() != chemical::aa_cys || rsd2.aa() != chemical::aa_cys ) return;

CentroidDisulfideEnergy.cc
130: if ( rsd1.aa() != chemical::aa_cys || rsd2.aa() != chemical::aa_cys ) return;

There may be other relevant code in the disulfide-creation machinery.

Line numbers are SVN 52071.
It is not clear to me that DCYD should be energetically equivalent to L-disulfides. Certainly the SG-SG term dslf_ss_dst is the same. The angle dslf_cs_ang is probably the same. I don't know about the dihedrals, but from the commentary in FullatomDisulfidePotential.cc it seems the potentials are roughly symmetric, implying that they are not "perfect" for D-disulfides but better than just refusing to handle D-disulfides.
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Issue History
2012-11-08 09:31smlewisNew Issue
2017-08-07 19:56amw579Fixed in SVN Version => n/a
2017-08-07 19:56amw579Statusnew => closed
2017-08-07 19:56amw579Assigned To => amw579
2017-08-07 19:56amw579Resolutionopen => fixed

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