用Packmol创建了含膜蛋白的生物膜系统，但无法在amber中正常运行，请求帮助

Kamala

1.用packmol构建初始体系，构建出来的体系如下图

2.问题1.
用charmmlipid2amber.py命令后，显示Error: No residues substituted。网上查询问题未果
3.问题2
直接用packmol得到的out.pdb文件进行tleap，显示了诸如FATAL:  Atom .R<UNK 13596>.A<H 5> does not have a type无数个

以下是我的 leap.in文件
source leaprc.lipid14
source leaprc.water.tip3p
source leaprc.protein.ff14SB
loadamberparams frcmod.ionsjc_tip3p
POPC = loadpdb POPC.pdb
set POPC box { 84.7270013689994837 84.4569962620735181 101.4770009517669678 }
saveAmberParm POPC POPC.prmtop POPC.inpcrd
quit

请教诸位，我哪个地方做得有错，如何纠正

Kamala

rpestana94 发表于 2021-8-6 22:29
you can try with charmm-gui to built the system, it will give you the amber files ready or try to er ...

是 packmol走不通，我现在在用charmm_gui，感谢回复！

rpestana94

you can try with charmm-gui to built the system, it will give you the amber files ready or try to erase all the hydrogen in your system and let leap add them for you, as I can see the error comes from an hydrogen