计算化学公社

标题: MCPB.py构建含金属离子蛋白力场参数时tleap报错找不到原子类型vdW参数生成不了top文件 [打印本页]

作者
Author: kepler_ye 时间: 2022-3-21 17:49
标题: MCPB.py构建含金属离子蛋白力场参数时tleap报错找不到原子类型vdW参数生成不了top文件
按照帖子http://bbs.keinsci.com/thread-26531-1-1.html做一个含Zn离子的蛋白，生成tleap.in文件内容如下：
source leaprc.protein.ff19SB
source leaprc.gaff
source leaprc.water.tip3p
loadoff atomic_ions.lib
addAtomTypes {
      { "M1"  "Zn" "sp3" }
      { "Y1"  "N" "sp3" }
      { "Y2"  "O" "sp3" }
      { "Y3"  "N" "sp3" }
      { "Y4"  "O" "sp3" }
}
loadoff ZN1.lib
loadoff ML1.lib
loadoff ML2.lib
loadoff HD1.lib
loadoff HD2.lib
loadoff AP1.lib
HD1 = loadmol2 HD1.mol2
AP1 = loadmol2 AP1.mol2
HD2 = loadmol2 HD2.mol2
ML1 = loadmol2 ML1.mol2
ZN1 = loadmol2 ZN1.mol2
ML2 = loadmol2 ML2.mol2
loadamberparams AKG.frcmod
loadamberparams MOL.frcmod
loadamberparams frcmod.ions1lm_126_tip3p
loadamberparams Ft_Zn_B_mcpbpy.frcmod
mol = loadpdb Ft_Zn_B_mcpbpy.pdb
bond mol.124.NE2 mol.286.ZN
bond mol.126.OD1 mol.286.ZN
bond mol.200.NE2 mol.286.ZN
bond mol.285.O5 mol.286.ZN
bond mol.123.C mol.124.N
bond mol.124.C mol.125.N
bond mol.125.C mol.126.N
bond mol.126.C mol.127.N
bond mol.199.C mol.200.N
bond mol.200.C mol.201.N
savepdb mol Ft_Zn_B_dry.pdb
saveamberparm mol Ft_Zn_B_dry.prmtop Ft_Zn_B_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol Ft_Zn_B_solv.pdb
saveamberparm mol Ft_Zn_B_solv.prmtop Ft_Zn_B_solv.inpcrd
quit

lib文件是通过下面方式生成的
tleap
ML2 =loadmol2 ML2.mol2
saveoff ML2 ML2.lib
...

但最后运行tleap的时候还是报错，信息如下：
/public1/home/sc90351/software/amber20/bin/teLeap: Warning!
Converting C-terminal residue name to PDB format: CSER -> SER
Checking Unit.
Building topology.
Building atom parameters.

/public1/home/sc90351/software/amber20/bin/teLeap: Error!
For atom (.R<HD1 124>.A<NE2 10>) could not find vdW (or other) parameters for type (Y1)

/public1/home/sc90351/software/amber20/bin/teLeap: Error!
For atom (.R<AP1 126>.A<OD1 7>) could not find vdW (or other) parameters for type (Y2)

/public1/home/sc90351/software/amber20/bin/teLeap: Error!
For atom (.R<HD2 200>.A<NE2 10>) could not find vdW (or other) parameters for type (Y3)

/public1/home/sc90351/software/amber20/bin/teLeap: Error!
For atom (.R<ML1 285>.A<O5 10>) could not find vdW (or other) parameters for type (Y4)

/public1/home/sc90351/software/amber20/bin/teLeap: Error!
For atom (.R<ZN1 286>.A<ZN 1>) could not find vdW (or other) parameters for type (M1)

/public1/home/sc90351/software/amber20/bin/teLeap: Warning!
Parameter file was not saved.
      Quit
请问怎么解决找不到原子类型vdW参数的问题，谢谢。

作者
Author: yjb 时间: 2023-3-16 20:41
你好，我也遇到了这个问题，我发现是mcpbpy.pdb文件里面把原先文件里面的残基名字改了，不知道你有没有解决这个问题？是不是可以通过做很多的lib文件解决呢？

欢迎光临计算化学公社 (http://bbs.keinsci.com/)