Dataset from "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2‑like Peptides"

Dataset from "Venomous Peptides: Molecular Origin of the Toxicity of Snake Venom PLA2‑like Peptides", containing the most relevant all-atom output trajectories and input files ran with GROMACS 2021:

1) pure_membrane_systems.7z - pure bilayer systems (AA1, AA2, AA5), including equilibration, calcium insertion, and umbrella sampling simulations;

2) single_peptide_systems.7z - single peptide-containing systems (AA3, AA4, AA6), including equilibration, calcium insertion, and umbrella sampling simulations;

3) multiple_peptide_systems.7z - multiple peptide-containing systems (AA7, AA8), including equilibration, calcium insertion, and umbrella sampling simulations.

We have included the input files (.mdp), system topology (.top and .itp), initial and final structure files (.gro), the index file (.ndx), and the portable binary run input files (.tpr). We have also included the output trajectories of systems AA3, AA4, AA6-8 in .xtc format, and spaced every 500 ps.

System composition is given in Table Z1. More details can be found in the related publication.

Table Z1. Simulated systems' details, including name, composition (in number of lipid and peptide molecules), number of atoms composing the systems, simulation (sim.) time, and total umbrella sampling (US) time. 

System
POPC/POPS/Peptide
no. atoms (a)
sim. time (µs)
US time (µs)

AA1
128/0/0
40,226
0.3
10.8

AA2
0/128/0
39,458
0.3
10.8

AA3
128/0/1
40,504
0.5
32.3

AA4
0/128/1
39,724
0.5
32.3

AA5
96/32/0
40,034
1.0
-

AA6
96/32/1
40,300
1.0
-

AA7
96/32/5
41,364
1.0
10.8

AA8
96/32/13
55,128
2.0
10.8

(a) for the US simulations, the total number of atoms was reduced in 1 because two sodium ions were substituted by a single calcium ion.