gmx distance -s md_0_10.tpr -f md_0_10_center.xtc -select 'resname "JZ4" and name OAB plus resid 102 and name OE1' -oall 得到的平均距离是0.31± 0.05 nm,于氢键形成的标准一致。 第二个判断氢键形成的标准是供体氢原子与受体原子之间的夹角。有很多不同的计算该夹角的惯例方法。在GROMACS的...
Tools like GROMACS, AMBER, CHARMM-GUI, and NAMD are the most widely used methods for MD simulation that can provide precise information on the motions and flexibility of a protein, which contributes to the interaction dynamics of protein鈥搇igand complexes. MD simulation has several other ...
80. Benchmarks tests performed with the program package Gromacs (version 2018)81showed that Martini based MD simulations of protein-ligand systems can be 110–350 times faster than all-atom simulations, with the performance gain increasing with growing system size (see SupplementaryDiscussionand ...
到这里预处理快结束了,接下来要做的是用openbabel去构建一个mol2文件,这个文件主要的目的是提供小分子的键合信息,你要是让网站自己去猜哪些原子成键了,大概率会出来一个四不像,再或者就是报错,所以话不多说,打开Terminal,输入如下代码: obabel -ipdb ligand.pdb -omol2 -O ligand.mol2 --minimize10000--ff ...
To gain insight into the structural dynamics of INSRTR structures, we performed MDS with a luciferase protein model using CHARMM27 all-atom force field embedded in GROMACS simulation package41. INSRTR models were prepared by inserting a loop into a wild-type protein fold (PDB ID: 1BA3) usin...
The accurate calculation of the binding free energy for arbitrary ligand–protein pairs is a considerable challenge in computer-aided drug discovery. Recently, it has been demonstrated that current state-of-the-art molecular dynamics (MD) based methods are capable of making highly accurate predictions...
(T4 lysozyme L99A/M102Q) in complex with a ligand. This tutorial focuses specifically on issues related to dealing with the ligand, assuming that the user is familiar with basic GROMACS operations and the contents of a topology. If this is not the case, please refer toa more basic tutorial...
The FGF signaling is generated by the binding of the ligand (FGF) to the extracellular domain of the FGFR, this binding induces dimerization of FGFR, which is an essential step in FGF signaling. Fibroblast growth factor receptor (FGFR) extracellular domain consists of three Ig domains D1, D2...
1)19,20. However, our MD simulations of ligand-bound GlnBP have sampled a broad conformational space beyond the crystal structures. The simulation was initiated from the crystal structure20 of ligand-bound GlnBP (closed conformation), followed by several rounds of simulations (~60 µs) to...
expression for structural studies, etc. Further, PPI are intricate processes, and its molecular details cannot be fully explained by experimental observations. Here, we describe a quick and simple method to study the PPI using the combinatorial approach of molecular dynamics simulation and biophysical ...