Amber学习第四天：Using Antechamber to Create Leap Input Files
Antechamber：能产生prmtop and inpcrd 文件用于蛋白－配体复合物的模拟。能解决以下问题：
1.自动的识别键于原子；2.判断原子的平衡。3.产生残基拓扑恩文件。4.寻找丢失的力场参数。
以Sustiva为例：
1）为Sustiva创建参数和坐标文件：
首先为从the RT-sustiva复合物中获取的Sustiva.pdb文件加氢：reduce sustiva.pdb > sustiva_h.pdb
为了与pdb文件的相一致，把文件中的"EFZ" 换为 "SUS"，产生sustiva_new.pdb文件。
为了创建"mol2" 文件, 需要在leap中定义一个新的单元。运行以下命令：
antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
-i sustiva.pdb specifies the name of the 3D structure file and the -fi pdb tells antechamber that this is a pdb format file；
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
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.
我们用parmchk来测试是否所有的参数是可用的;
parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod 运行这个产生sustiva.frcmod文件,导入到leap中增加丢失的参数。
We now have everything we need to load sustiva as a unit in Leap：
$tleap -f leaprc.ff99SB
>source leaprc.gaff
Now we can load our sustiva unit (sustiva.mol2):
>SUS = loadmol2 sustiva.mol2
如果输入list会在表中看见SUS这个单元。
>check SUS
>loadamberparams sustiva.frcmod
检查完创建(sus.lib)和(sustiva.prmtop, sustiva.inpcrd)文件
>saveoff SUS sus.lib
>saveamberparm SUS sustiva.prmtop sustiva.inpcrd
以上的这些命令也可以写成一个脚本：如tleap.in
source leaprc.ff99SB
source leaprc.gaff
SUS = loadmol2 sustiva.mol2
check SUS
loadamberparams sustiva.frcmod
saveoff SUS sus.lib
saveamberparm SUS sustiva.prmtop sustiva.inpcrd
quit
通过运行tleap -f tleap.in这个就可以做以上的操作。
2）为Sustiva-RT 复合物创建 topology and coordinate文件：
复合物的文件:1FKO_trunc.pdb.
为了让1FKO pdb文件能被tleap识别，所以要改变文件中残基EFZ 到 SUS。因为库中含有相同的残基。产生文件：1FKO_trunc_sus.pdb
tleap -f leaprc.ff99SB
>source leaprc.gaff
>loadamberparams sustiva.frcmod
Now we load the Sustiva library file (sus.lib), followed by the complex pdb file 1FKO_trunc_sus.pdb.
>loadoff sus.lib
>complex = loadpdb 1FKO_trunc_sus.pdb
Finally, we are ready to create our topology and coordinate files of the truncated RT-sustiva complex.
>saveamberparm complex 1FKO_sus.prmtop 1FKO_sus.inpcrd
>savepdb complex 1FKO_sus.pdb
>quit
3）Minimize and Equilibrate the Sustiva-RT complex
首先最小化复合物来去除坏的作用。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
运行：sander -O -i min.in -o 1FKO_sus_min.out -p 1FKO_sus.prmtop -c 1FKO_sus.inpcrd -r 1FKO_sus_min.crd &
产生最小化的pdb文件:ambpdb -p 1FKO_sus.prmtop <1FKO_sus_min.crd > 1FKO_sus_min.pdb
Here's our input file, we will run MD (imin=0) and this is not a restart (irest=0).
eq.in
Initial MD equilibration
&cntrl
imin=0, irest=0,
nstlim=1000,dt=0.001, ntc=1, //I will use a time step of 1 fs and run for 1000 steps
ntpr=20, ntwx=20, //write to our output file every 20 steps and to our trajectory [mdcrd] file every 20 steps (ntpr=20,ntwx=20)
cut=16, ntb=0, igb=1,
ntt=3, gamma_ln=1.0, //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).
tempi=0.0, temp0=300.0,
&end
Now we run:
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
The heating trajectory and restart coordinates are saved in 1FKO_sus_eq.mdcrd and 1FKO_sus_eq.rst, respectively. Now that the sustiva-RT complex is minimized and heated, you can take a look at the snapshot at 300K. This structure can be used as the starting point for further equilibration.
