标题: 求助：使用MCPB.py构建含铁蛋白的立场参数，tleap阶段缺失了键二面角等参数 [打印本页] 作者Author: a414164396 时间: 2025-1-30 19:55 标题: 求助：使用MCPB.py构建含铁蛋白的立场参数，tleap阶段缺失了键二面角等参数 我想构建一个含铁蛋白质的amber力场参数，使用amber自带的MCPB.py文件进行构建。
使用高斯16进行建模之后，通过MCPB.py的step1-4生成了蛋白质的frcmod文件和各个残基/配体及铁离子的mol2文件后，通过tleap生成拓扑文件时报错
/home/wangmengyang/miniforge3/envs/gmxMMPBSA/bin/teLeap: Error!
Could not find bond parameter for atom types: NB - H4
for atom NE2 at position 2.406000, -5.215000, 1.231000
and atom HD2 at position 3.264000, -5.606000, 0.601000.
/home/wangmengyang/miniforge3/envs/gmxMMPBSA/bin/teLeap: Error!
Could not find bond parameter for atom types: CV - H5
for atom CD2 at position 2.939000, -5.417000, 2.506000
and atom HE1 at position 3.856000, -5.815000, 2.914000.
/home/wangmengyang/miniforge3/envs/gmxMMPBSA/bin/teLeap: Error!
Could not find bond parameter for atom types: Y2 - CV
for atom ND1 at position 1.986000, -4.968000, 3.323000
and atom CD2 at position 2.939000, -5.417000, 2.506000.
/home/wangmengyang/miniforge3/envs/gmxMMPBSA/bin/teLeap: Error!
Could not find bond parameter for atom types: CR - H
for atom CE1 at position 0.907000, -4.518000, 2.679000
and atom HD1 at position -0.033000, -4.109000, 3.020000.
/home/wangmengyang/miniforge3/envs/gmxMMPBSA/bin/teLeap: Error!
Could not find bond parameter for atom types: CC - CR
for atom CG at position 1.153000, -4.649000, 1.325000
and atom CE1 at position 0.907000, -4.518000, 2.679000.
Building angle parameters.
/home/wangmengyang/miniforge3/envs/gmxMMPBSA/bin/teLeap: Error!
Could not find angle parameter for atom types: NB - CV - H5
for atom NE2 at position 2.406000, -5.215000, 1.231000,
atom CD2 at position 2.939000, -5.417000, 2.506000,
and atom HE1 at position 3.856000, -5.815000, 2.914000.
/home/wangmengyang/miniforge3/envs/gmxMMPBSA/bin/teLeap: Error!
Could not find angle parameter for atom types: CV - NB - H4
for atom CD2 at position 2.939000, -5.417000, 2.506000,
atom NE2 at position 2.406000, -5.215000, 1.231000,
and atom HD2 at position 3.264000, -5.606000, 0.601000.
检查后发现缺失的这些键和二面角信息都是和金属配合的氨基酸残基和配体原子，想请教一下大家为什么会出现这种情况呢作者Author: Huschein 时间: 2025-1-31 03:00
AMBER力场没有这些不是很正常吗 自己手动找文献参数补到frcmod就行作者Author: rootczy 时间: 2025-5-17 09:59
您好，我也遇到了这样的问题，请问解决了吗作者Author: 18217265596 时间: 2025-5-18 20:59