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
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