Bogdan I. Iorga

BioF class B2 beta-lactamase should get a PFM allele number ?

1

A paper describing a new class B2 beta-lactamase named BioF has just come out ("BioF is a novel B2 metallo-β-lactamase from _Pseudomonas_ sp. isolated from an on-farm biopurification system", Environ...

In the Lahey repository, the allele number was assigned to a partial sequence for [OXA-410](https://www.ncbi.nlm.nih.gov/protein/AJD77428) (last residue missing). Now a [complete sequence](https://www.ncbi.nlm.nih.gov/protein/HCT5551642.1) is available, which should replace the old one.

Currently some scripts (e.g. `mdpow-rebuild-fep`) do not have implemented the new solvents (cyclohexane, toluene). All solvents should be implemented (water, octanol, cyclohexane, toluene) should be implemented in all scripts.

incompatible residue names for OPLS ions

6

I tried to set up a simulation using a positively charged ligand (with Gromacs 4.6) and I've got the following error. ``` gromacs.setup: INFO Solvated system with tip4p.gro gromacs.cbook: INFO...

add user-defined maxwarn options to all steps (EM, MD_relaxed, MD_NPT)

2

Currently, maxwarn option can be set up only for FEP (see #113). We need that user can change it in all steps (via the `runinput.yml` file), so this option should...

no backwards compatibility for the "watermodel" option of configuration file

3

The "watermodel" option of the configuration file that was present originally in MDPOW was replaced by the more general "solventmodel". Currently, when the "watermodel" option is present in the configuration...

Species discrepancy for OXA-258-like class D beta-lactamase OXA-1251

3

Dear all, Historically, all OXA-258-like beta-lactamases were found in _Achromobacter_ spp., one [paper](https://doi.org/10.1128/jcm.03043-12) considering OXA-258 as a species-specific marker for _Achromobacter ruhlandii_. [OXA-1251](https://www.ncbi.nlm.nih.gov/protein/XBP46887.1) has 99.3% sequence identity with OXA-258, and...

FRI-8 beta-lactamase should be renamed as FLC-2 ?

4

Hello, The [FRI-8](https://www.ncbi.nlm.nih.gov/protein/WP_140423308) beta-lactamase (described in this [paper](http://dx.doi.org/10.1089/mdr.2022.0123)) has 99.6 % sequence identity with [FLC-1](https://www.ncbi.nlm.nih.gov/protein/WP_123061077), whereas it has only 81 % sequence identity with [FRI-1](https://www.ncbi.nlm.nih.gov/protein/WP_063860498). Additionally, the N-terminal sequence is...

Hello, When a custom fast temporary directory is selected with the option `--tmpdir`, this is not used by kmc, which uses the default tmp directory instead. ``` [dragonflye] You ran:...

Hello, With FASTQ files generated by `dorado demux --emit-fastq` kmc (I am using KMC 3.2.4) doesn't work correctly: ``` ~/temp_test > cat dorado.fastq @924f595d-fb8d-473e-bb99-b554dfdd5ce9 st:Z:2024-09-11T03:04:06.675+00:00 RG:Z:41b0457e40e383b3df64af4d8e649576ca9a4668_dna_r10.4.1_e8.2_400bps_fast@v5.0.0 GAAGCGACAGCGTATGCGCGTGTTTAAGTTCGACTGGTTCTCTGCCACCGGTACCGCCATTCTTTTTGCTGCCCTGCTCTCGATTGTCTGGCTGAAGATGAAACCATCTGACGCTATCAGCGCCTTCGGCAGCACGCTGAAGGACTGGCTCTGCCTATCTACTCCATCGGTATGGTGCTGGCGTTCGCCTTTATCTCGAACTATTCCGGACTATCATCAACGCTGGCGCTGGCGCTCGCACACACCGGCCATGCATTCCGCCTTTTCTCTCTCGCCGTTCCTCGGCTGGCTTGGTGTCTTCCTGACCGGATCGGATACCTCATCTAACGCCCTGTTCGCCGCCCTGCAAGCCGCTGCAGCACAACAAATTGGCGTTTCTGACCTGTTGTTGGTTGCCGCCAACACCGCCGGTGGTGTCGCCGGTTAAGATGATCTCTTCCGCAATCTATCGCTATCACCTATGCGGGGATAGGCGTGGTAGGCAAAGAGTCAGATCTCTCGCTTTACCATCAAACGCAGCTAAATCTCACCTGTATGGTCGGCGTGATCGCCACGCTCAGGCTTATGTCTTAACGTGGATAATTTGCTAATGATTGTTTTACCCAGACGCCTGTCAGACAAGGTCCGATCGTGTGCGGGCGCTGATGGTGATG + 89D>AABD:9:2106.-&)'))**4495@50'&'7.99=54166AH@A>=D>86789A=>=ADSDMIHB@>??BG?=656M@9869711A??>>:99@888B58))*= kmc...