标题: 求助AMBER99SB-ILDN 力场的ions.mdp文件怎么写 [打印本页] 作者Author: awjido 时间: 2024-12-25 21:21 标题: 求助AMBER99SB-ILDN 力场的ions.mdp文件怎么写 想将设计的蛋白质疫苗序列与TLR受体做分子动力学模拟，由于都是蛋白质，就都放到一个PDB文件里做的，采用的AMBER99SB-ILDN 力场，TIP3P水模型，没有找到这个力场的ions.mdp文件，现在用的这个输入后不能用。想请教下大家有没有AMBER99SB-ILDN 力场的ions.mdp文件
; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching (Verlet scheme)
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Use PME for long-range electrostatics
rcoulomb = 1.0 ; Short-range electrostatic cut-off (in nm)
rvdw = 1.0 ; Short-range Van der Waals cut-off (in nm)
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
; Electrostatics (for PME)
pme_order = 4 ; PME interpolation order
fourierspacing = 0.16 ; Grid spacing for PME