Amber TUTORIAL 4b: Using Antechamber to Create LEaP Input Files for Simulating Sustiva (efavirenz)-R

Posted 2020-11-14 wq242424

sustiva.pdb

PDB: 1FKO

Create parameter and coordinate files for Sustiva

1. 加氢：

 

reduce sustiva.pdb > 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 2

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：

开启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

开启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未见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=1, maxcyc=200, ncyc=50,
  cut=16, ntb=0, igb=1,
 &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 <1FKO_sus_min.crd > 1FKO_sus_min.pdb