||
(四)添加盒子
$gmx/editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0
** -f 输入复合物的gro文件
** -o 输出含盒子的结构文件,newbox.gro
** -bt 定义水盒子形状:triclinic(三斜体), cubic(立方体), dodecahedron(十二面体),octahedron(八面体)
** -d 定义盒子的尺寸,即盒子边缘距离分子边缘的距离(单位:nm),通常不能小于0.85nm。
(五)在盒子中放入溶剂
$gmx/genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
** -cp newbox.gro 输入含盒子的结构文件
** -cs spc216.gro 指定spc水盒子
** -p topol.top 输出含溶剂的复合物top文件,文件名不变topol.top
** -o solv.gro 输出含溶剂的复合物gro文件,文件名solv.gro
(六)编写能量最小化配置文件em.mdp
用记事本编写如下参数,保存为em.mdp
; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run
; 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 < 10.0 kJ/mol
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
energygrps = system ; Which energy group(s) to write to disk
; 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
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
(七)grompp预处理
$gmx/grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
** -f em.mdp 指定配置文件
** -c solv.gro 指定输入的结构文件
** -p topol.top 指定输入的top文件
** -o ions.tpr 输出用来运行mdrun的tpr文件
此时注意到系统提示带6个正电荷:
NOTE 2 [file topol.top, line 10674]:
System has non-zero total charge: 6.000001
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
(八)添加抗衡离子
$gmx/genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6
** -s ions.tpr 输入预处理得到的tpr文件
** -o solv_ions.gro 输出添加了抗衡离子后的gro结构文件
** -p topol.top 输出top文件
** -pname NA 添加的阳离子类型
** -nname CL 添加的阴离子类型
** -nn 6 添加阴离子的个数
此时注意到系统提示“Select a continuous group of solvent molecules”,选择溶剂,即:
Group 15 ( SOL) has 31341 elements
系统自动将溶剂中的某些原子用氯来代替。
并且可以发现topol.top 文件中增加了溶剂和抗衡离子项:
[ molecules ]
; Compound #mols
Protein_chain_A 1
JZ4 1
SOL 10441
CL 6
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