gromacs输出的pdb文件加氢数目不对怎么办

Yoghurt

用GMX跑完蛋白质的动力学，trjconv出pdb文件，发现每个残基HIS上的芳香环上的一个N原子都多加一个H（真实应该是NC双键，但是输出的默认为单键，因此自动补氢的时候N上多出一个H），请问如何能避免这种问题？谢谢

puzhongji

AMBER Histidine residues
Histidine (HIS in normal pdb files) is really one of three possible residues:
HID: Histidine with hydrogen on the delta nitrogen
HIE: Histidine with hydrogen on the epsilon nitrogen
HIP: Histidine with hydrogens on both nitrogens; this is positively charged.
It is up to the user to inspect the environment of each histidine and identify the type that is appropriate.

sobereva

trjconv过程本身不会修改结构。弄清楚导致氢不对是哪步所致。pdb文件里本身不记录形式键