Amber TUTORIAL 4b: Using Antechamber to Create LEaP Input Files for Simulating Sustiva (efavirenz)-RT complex using the General Amber Force Field (GAFF)

Create parameter and coordinate files for Sustiva

1. 加氢：

$ reduce sustiva.pdb > sustiva_h.pdb

sed -i s/"EFZ"/"SUS"/g sustiva_h.pdb

加氢完毕后把文件内所有“EFZ”换为“SUS”。

2.转换为mol2格式：

$ antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s

Here the -i sustiva.pdb specifies the name of the 3D structure file and the -fi pdb tells antechamber that this is a pdb format file (we could easily have used any number of other supported formats including Gaussian Z-Matrix [gzmat], Gaussian Output [gout], MDL [mdl], amber Restart [rst], Sybyl Mol2 [mol2]). The -o sustiva.mol2 specifies the name of our output file and the -fo mol2 states that we want the output file to be of Tripos Mol2 format (this is an internal format supported by LEaP). The -c bcc option tells antechamber to use the AM1-BCC charge model in order to calculate the atomic point charges while the -s 2 option defines the verbosity of the status information provided by antechamber. In this case we have selected verbose output (2).

3.用parmchk检查参数的可用性：

$ parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod

此命令产生参数文件sustiva.frcmod

We can see that there were a total of 4 missing angle parameters and 4 missing improper dihedrals in "sustiva.frcmod". For the purposes of this tutorial we shall assume that the parameters Antechamber has suggested for us are acceptable. Ideally you should really test these parameters (by comparing to ab initio calculations for example) to ensure they are reasonable. If you see any parameters listed with the comment "ATTN: NEEDS REVISION" then it means that Antechamber could not determine suitable parameters and so you must manually provide these before you can proceed with the simulation. By default Antechamber will have set the values to zero.

4.加载sustiva到LEaP中：

打开LEaP：

$ tleap -f oldff/leaprc.ff99SB

加载：

> source leaprc.gaff

> SUS = loadmol2 sustiva.mol2 

> check SUS

> loadamberparams sustiva.frcmod

> check SUS

> saveoff SUS sus.lib 

> saveamberparm SUS sustiva.prmtop sustiva.inpcrd

Creating topology and coordinate files for Sustiva-RT complex

1FKO_trunc_sus.pdb

1.LEaP

打开LEaP

$ tleap -f oldff/leaprc.ff99SB

载入参数：

> source leaprc.gaff
# 加载sustiva力场参数文件

> loadamberparams sustiva.frcmod

> loadoff sus.lib

# 再加载复合物

> complex = loadpdb 1FKO_trunc_sus.pdb

# 保存

> saveamberparm complex 1FKO_sus.prmtop 1FKO_sus.inpcrd 

> savepdb complex 1FKO_sus.pdb

> quit

也可把上述命令存为tleap2.in，使用 tleap -f tleap2.in 产生复合体pdb。

Minimize and Equilibrate the Sustiva-RT complex

1.准备优化输入文件:

$$$ min.in

Initial minimisation of sustiva-RT complex

 &cntrl

  imin=, maxcyc=, ncyc=,

  cut=, ntb=, igb=,

 &end

2.运行优化程序：

sander -O -i min.in -o 1FKO_sus_min.out -p 1FKO_sus.prmtop -c 1FKO_sus.inpcrd  -r 1FKO_sus_min.crd  &

3.查看pdb：

ambpdb -p 1FKO_sus.prmtop -c 1FKO_sus_min.crd > 1FKO_sus_min.pdb

4.准备MD run文件：

$$$ eq.in

Initial MD equilibration

 &cntrl

  imin=, irest=,

  nstlim=,dt=0.001, ntc=,

  ntpr=, ntwx=,

  cut=, ntb=, igb=,

  ntt=, gamma_ln=1.0,

  tempi=0.0, temp0=300.0,

 &end

We will run MD (imin=0) and this is not a restart (irest=0). In this example we will not use shake since it is possible that the hydrogen motion may effect the binding energy (probably not, but it serves as an example here). As we are not using shake we will need a time step smaller than normal. Here I will use a time step of 1 fs and run for 1000 steps [2 ps] (dt = 0.001, nstlim=1000, ntc=1). We will also write to our output file every 20 steps and to our trajectory [mdcrd] file every 20 steps (ntpr=20,ntwx=20). For temperature control we will use a Langevin dynamics approach with a collision frequency of 1 ps^-1. We will start our system at 0K and we want a target temperature of 300K (ntt=3, gamma_ln=1.0, tempi=0.0, temp0=300.0).

5.heat && equilibrium

sander -O -i eq.in -o 1FKO_sus_eq.out -p 1FKO_sus.prmtop -c 1FKO_sus_min.crd  -r 1FKO_sus_eq.rst -x 1FKO_sus_eq.mdcrd &

6.查看pdb：

ambpdb -p 1FKO_sus.prmtop -c 1FKO_sus_eq.mdcrd > 1FKO_sus_eq.pdb