求助tLeap在保存crd文件时与同时保存的pdb分子坐标有差异

Zachariah

在tleap中，想要导入一个水分子，该水分子在tleap中被定义为w1，已经溶剂化的蛋白质被定义为nap

执行：
frcc=combine {nap w1}

saveamberparm frcc macro.top macro.crd
savepdb frcc macro.pdb


保存的macro.pdb显示水分子的坐标为：

ATOM  49903  O   WAT  15135    -18.145  22.287  32.483  1.00  0.00
ATOM  49904  H1  WAT  15135    -18.331  22.096  31.519  1.00  0.00
ATOM  49905  H2  WAT  15135    -18.049  21.419  32.977  1.00  0.00


但在使用ambpdb -p top -c crd > pdb命令后，得到的pdb该分子的坐标却是这样的
ATOM  49903  O   WAT  5135      26.853  67.285  77.481  1.00  0.00           O
ATOM  49904  H1  WAT  5135      26.667  67.094  76.517  1.00  0.00           H
ATOM  49905  H2  WAT  5135      26.949  66.417  77.975  1.00  0.00           H


请问产生该问题的原因是什么呢

rpestana94

If you only need the pdb, have you tried using cpptraj to get it from the top and crd? Maybe in this way you won't have that error

Zachariah

rpestana94 发表于 2023-8-15 21:09
If you only need the pdb, have you tried using cpptraj to get it from the top and crd? Maybe in this ...

Thanks for the reply, I have tried generating crd file and top file using .pdb, but found that the Periodic box parameters are lost