ACEMD之利用HTMD构建膜蛋白体系

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随着近年来计算机软硬件技术的发展，利用分子动力学模拟研究膜蛋白体系越来越多。因此，如何构建膜蛋白体系就显得尤其重要。众多的分子动力学模拟软件中，ACEMD作为一款新的分子动力学软件，基于Python环境的HTMD能够使用户更便捷的构建膜蛋白体系并应用于HTMD和ACEMD软件进行分子动力学模拟。

building protein in membrane

#!/usr/bin/python3

# coding: utf-8

# In[1]:导入模块，开启可视化

from htmd.ui import *

config(viewer='ngl')

# In[2]:准备蛋白并可视化

Molecule('mor/4dkl.pdb').view()

# In[3]:清理蛋白结构

from htmd.util import opm

prot, thickness = opm('4dkl')

thickness

# In[4]:清理非蛋白结构

prot.filter('protein and noh and chain B or water within 5 of (chain B and protein)')

# In[5]:自动检测片段并重命名

prot = autoSegment(prot,'protein')

# In[6]:建立蛋白坐标和拓扑

topos = charmm.defaultTopo() + ['mor/ff.rtf']

params = charmm.defaultParam() + ['mor/ff.prm']

prot = charmm.build(prot, topo=topos, param=params,

outdir='./03c_out_morbuild/prot/', ionize=False)

# In[7]:可视化设置

# In[8]:添加离子

sod = Molecule('mor/sod.pdb')

sod.set('segid','S1')

prot.append(sod)

prot.reps.add(sel='ions', style='VDW')

prot.view()

# In[9]:载入膜结构

memb=Molecule('mor/membrane80by80C36.pdb')

# In[10]:将膜至于蛋白中心

pcenter=np.mean(prot.get('coords','protein'),axis=0)

mcenter=np.mean(memb.get('coords'),axis=0)

memb.moveBy(pcenter-mcenter)

# In[11]:蛋白嵌入膜

mol = prot.copy()

mol.append(memb, collisions=True)

# mol = embed(prot,memb)

# In[12]:可视化膜蛋白系统

# In[13]:向膜蛋白中加入配体

lig = Molecule('mor/QM-min.pdb')

lig.set('segid','L');

lcenter = np.mean(lig.get('coords'),axis=0)

newlcenter=[np.random.uniform(-10, 10), np.random.uniform(-10, 10), 43 ]

lig.rotateBy(uniformRandomRotation(), lcenter)

lig.moveBy(newlcenter-lcenter)

mol.append(lig)

# In[14]:添加水盒子

coo = mol.get('coords','noh and (lipids or protein)')

m = np.min(coo, axis=0) + [0, 0, -5]

M = np.max(coo, axis=0) + [0, 0, 20]

smol = solvate(mol, minmax=np.vstack((m,M)))

# In[15]:可视化

# In[16]:建立蛋白的charmm力场坐标和拓扑

molbuilt = charmm.build(smol, topo=topos, param=params,

outdir='./build/',

saltconc=0.15)

# In[17]:建立后体系可视化

molbuilt.view()

参考资料

https://software.acellera.com/docs/latest/htmd/tutorials/system-building-protein-in-membrane.html

https://software.acellera.com/docs/latest/htmd/tutorials/protein-preparation.html

https://software.acellera.com/docs/latest/htmd/userguide/advancedbuilding.html

http://gainstrong.net/works/hudong/