复合物-方便复制

conda activate ambertools
tleap
source leaprc.protein.ff19SB
source leaprc.phosaa10


source leaprc.gaff2  
source leaprc.water.opc 




loadamberparams /home/lywu/pengziyu/0103/t28-2/lig_4zy4-t28.frcmod
loadamberprep /home/lywu/pengziyu/0103/t28-2/lig_4zy4-t28.prep


mol = loadpdb 
pro = loadpdb 
com= combine {pro mol}


saveamberparm pro pro.prmtop pro.inpcrd
saveamberparm mol lig.prmtop lig.inpcrd
saveamberparm com native.prmtop native.inpcrd
savepdb com com-dry.pdb


charge com
solvatebox com OPCBOX 12
addionsrand com Na+ 15


saveAmberParm com complex.prmtop complex.inpcrd
savePdb com complex.pdb
quit

# AMBER 参数转 GMX 参数
#进入python 
import parmed as pmd
amber = pmd.load_file('complex.prmtop','complex.inpcrd')
amber.save('gmx.top')
amber.save('gmx.gro')

; Include Position restraint file
 #ifdef  POSRES
 #include "posre1.itp
 #endif