Comments (6)
Thanks. I had not seen the issue and really appreciate the heads-up.
To be clear for the issue tracker -- this is an issue with Yank setups which use the .mol2 files here, but not (necessarily) with the mol2 files themselves?
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this is an issue with Yank setups which use the .mol2 files here, but not (necessarily) with the mol2 files themselves?
Correct. To be more specific, this is an issue for any pipeline involving ParmEd manipulating host-bcd.mol2
and host-acd.mol2
(which include YANK's with no OpenEye charges). The other hosts should not be affected by the ParmEd's bug.
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Can you tell what triggers this (e.g. what other systems would be affected?)? It sounds like you're saying just receptors which are multi-residue mol2 files?
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(Out of curiosity, why are you using ParmEd's mol2 features at all? I've found various bugs there in the past.)
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It sounds like you're saying just receptors which are multi-residue mol2 files?
Correct, but only cyclic receptors that are multi-residue mol2 files.
why are you using ParmEd's mol2 features at all?
When the mol2
charges have some precision errors, we use parmed.modeller.residue.fix_charges()
to round the net charge to the nearest integer to avoid artifacts.
from benchmarksets.
Correct, but only cyclic receptors that are multi-residue mol2 files.
Sorry, and by "cyclic" here I mean that the first residue is bound to the last residue.
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Related Issues (20)
- Add README.md for host-guest inputs; add additional info
- Update text to reflect host-guest sets added in #22 HOT 1
- CD mol2 files coordinates starting in the binding pocket HOT 20
- Add additional supplementary data, perhaps in markdown files? HOT 5
- Get CD benchmarks in? HOT 3
- Provide suitable README files for CB7, GDCC benchmarks
- Provide bound-state starting structures for hosts HOT 5
- Deposit calculated values for provided files when available HOT 5
- Should we use table titles and not numbers in markdown files? HOT 6
- Provide compound ID for all files HOT 5
- Update README.md to reflect how to cite (once discussion is final) HOT 4
- Mixed 1-4 scaling? HOT 2
- Typo in reference for Lysozyme L99A/M102Q - catechol experimental value? HOT 3
- Errors using cyclic host `mol2` files with non-unique atom names HOT 11
- Add machine-readable tables for all the sets HOT 3
- The SDF files for charged compounds aren't listing the formal charges of the atoms HOT 2
- PDB files for BRD4 parameterized systems are missing CONECT records HOT 2
- Include additional data, references
- gdcc-set2 and CB experimental Delta H is missing HOT 4
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