Amber 中Lipid11 PDB文件的格式

      LIPID11中每个磷脂分子由3个残基组成。当在LEAP程序中加在磷脂的PDB文件时,LEAP程序就可以将分子的头部和尾部连接在一起。为了使LEAP能够正确的识别磷脂分子,

PDB中残基的定义方式应当按照下面的定义方法:

                                   PDB中的每一个磷脂分子的定义:

                                          

sn-1tailresidue
headgroupresidue
sn-2tailresidue
TER  

在将PDB载入LEAP的时候,应当将PDB文件中的CONECT信息删除,因为这些信息是冗余的。


  • 0
    点赞
  • 1
    收藏
    觉得还不错? 一键收藏
  • 0
    评论
MDAnalysis 分析分子动力学轨迹 MDAnalysis-0.7.2.tar.gz MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides an extremely flexible and relatively fast framework for complex analysis tasks. In addition, CHARMM-style atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out. A typical usage pattern is to iterate through a trajectory and analyze coordinates for every frame. In the following example the end-to-end distance of a protein and the radius of gyration of the backbone atoms are calculated: import MDAnalysis from MDAnalysis.tests.datafiles import PSF,DCD # test trajectory import numpy.linalg u = MDAnalysis.Universe(PSF,DCD) # always start with a Universe nterm = u.s4AKE.N[0] # can access structure via segid (s4AKE) and atom name cterm = u.s4AKE.C[-1] # ... takes the last atom named 'C' bb = u.selectAtoms('protein and backbone') # a selection (a AtomGroup) for ts in u.trajectory: # iterate through all frames r = cterm.pos - nterm.pos # end-to-end vector from atom positions d = numpy.linalg.norm(r) # end-to-end distance rgyr = bb.radiusOfGyration() # method of a AtomGroup; updates with each frame print "frame = %d: d = %f Angstroem, Rgyr = %f Angstroem" % (ts.frame, d, rgyr)
评论
添加红包

请填写红包祝福语或标题

红包个数最小为10个

红包金额最低5元

当前余额3.43前往充值 >
需支付:10.00
成就一亿技术人!
领取后你会自动成为博主和红包主的粉丝 规则
hope_wisdom
发出的红包
实付
使用余额支付
点击重新获取
扫码支付
钱包余额 0

抵扣说明:

1.余额是钱包充值的虚拟货币,按照1:1的比例进行支付金额的抵扣。
2.余额无法直接购买下载,可以购买VIP、付费专栏及课程。

余额充值