acpype生成小分子Amber力场报错

jollydai

老师们好！
我在使用acpype生成小分子Amber力场时报错，分子结构与报错信息如下，请问具体是什么原因？该如何处理才能生成Amber力场呢？谢谢！

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find bond parameter for atom types: OH - N*
for atom O at position -3.971000, 0.047000, -0.236000
and atom N2 at position -2.592000, 0.068000, -0.096000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find bond parameter for atom types: NT - CA
for atom N at position 1.425000, -0.208000, 0.347000
and atom C5 at position 0.082000, -0.154000, 0.203000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find bond parameter for atom types: N* - CQ
for atom N2 at position -2.592000, 0.068000, -0.096000
and atom C8 at position -1.995000, -1.163000, 0.101000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find bond parameter for atom types: N2 - CM
for atom N3 at position -2.501000, 2.476000, -0.352000
and atom C7 at position -1.888000, 1.264000, -0.156000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find bond parameter for atom types: DU - CQ
for atom N4 at position -2.636000, -2.293000, 0.160000
and atom C8 at position -1.995000, -1.163000, 0.101000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find bond parameter for atom types: DU - H
for atom N4 at position -2.636000, -2.293000, 0.160000
and atom H13 at position -1.956000, -3.046000, 0.313000.
Checking for angle parameters.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: OH - N* - CM
for atom O at position -3.971000, 0.047000, -0.236000,
atom N2 at position -2.592000, 0.068000, -0.096000,
and atom C7 at position -1.888000, 1.264000, -0.156000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: OH - N* - CQ
for atom O at position -3.971000, 0.047000, -0.236000,
atom N2 at position -2.592000, 0.068000, -0.096000,
and atom C8 at position -1.995000, -1.163000, 0.101000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: NT - CA - NC
for atom N at position 1.425000, -0.208000, 0.347000,
atom C5 at position 0.082000, -0.154000, 0.203000,
and atom N1 at position -0.624000, -1.258000, 0.252000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: NT - CA - CM
for atom N at position 1.425000, -0.208000, 0.347000,
atom C5 at position 0.082000, -0.154000, 0.203000,
and atom C6 at position -0.549000, 1.196000, -0.011000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: NC - CQ - N*
for atom N1 at position -0.624000, -1.258000, 0.252000,
atom C8 at position -1.995000, -1.163000, 0.101000,
and atom N2 at position -2.592000, 0.068000, -0.096000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: NC - CQ - DU
for atom N1 at position -0.624000, -1.258000, 0.252000,
atom C8 at position -1.995000, -1.163000, 0.101000,
and atom N4 at position -2.636000, -2.293000, 0.160000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: N* - OH - HO
for atom N2 at position -2.592000, 0.068000, -0.096000,
atom O at position -3.971000, 0.047000, -0.236000,
and atom H14 at position -4.269000, 0.176000, 0.681000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: N* - CM - N2
for atom N2 at position -2.592000, 0.068000, -0.096000,
atom C7 at position -1.888000, 1.264000, -0.156000,
and atom N3 at position -2.501000, 2.476000, -0.352000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: N* - CQ - DU
for atom N2 at position -2.592000, 0.068000, -0.096000,
atom C8 at position -1.995000, -1.163000, 0.101000,
and atom N4 at position -2.636000, -2.293000, 0.160000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: N2 - CM - CM
for atom N3 at position -2.501000, 2.476000, -0.352000,
atom C7 at position -1.888000, 1.264000, -0.156000,
and atom C6 at position -0.549000, 1.196000, -0.011000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: CT - NT - CA
for atom C3 at position 2.205000, -1.371000, -0.071000,
atom N at position 1.425000, -0.208000, 0.347000,
and atom C5 at position 0.082000, -0.154000, 0.203000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: CT - NT - CA
for atom C4 at position 2.176000, 0.848000, 1.024000,
atom N at position 1.425000, -0.208000, 0.347000,
and atom C5 at position 0.082000, -0.154000, 0.203000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: CM - N* - CQ
for atom C7 at position -1.888000, 1.264000, -0.156000,
atom N2 at position -2.592000, 0.068000, -0.096000,
and atom C8 at position -1.995000, -1.163000, 0.101000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: CM - N2 - H
for atom C7 at position -1.888000, 1.264000, -0.156000,
atom N3 at position -2.501000, 2.476000, -0.352000,
and atom H11 at position -1.954000, 3.327000, -0.390000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: CM - N2 - H
for atom C7 at position -1.888000, 1.264000, -0.156000,
atom N3 at position -2.501000, 2.476000, -0.352000,
and atom H12 at position -3.507000, 2.505000, -0.458000.

/home/jolly/miniconda3/bin/teLeap: Error!
Could not find angle parameter for atom types: CQ - DU - H
for atom C8 at position -1.995000, -1.163000, 0.101000,
atom N4 at position -2.636000, -2.293000, 0.160000,
and atom H13 at position -1.956000, -3.046000, 0.313000.

/home/jolly/miniconda3/bin/teLeap: Warning!
There are missing parameters.
Unit is OK.
Checking Unit.
Building topology.
Building atom parameters.

/home/jolly/miniconda3/bin/teLeap: Error!
For atom (.R<UNL 1>.A<N4 6>) could not find vdW (or other) parameters for type (DU)

/home/jolly/miniconda3/bin/teLeap: Warning!
Parameter file was not saved.
Saving UNL.
Building topology.
Building atom parameters.
        Quit

Exiting LEaP: Errors = 23; Warnings = 2; Notes = 0.
ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Tleap failed
==> Removing temporary files...
ERROR: Files 'MIN_AC.inpcrd' and/or 'MIN_AC.prmtop' don't exist
ERROR: molTopol object won't be created
ERROR: ACPYPE FAILED: [Errno 2] No such file or directory: 'MIN_AC.inpcrd'
Traceback (most recent call last):
  File "/home/jolly/miniconda3/lib/python3.10/site-packages/acpype/cli.py", line 140, in init_main
    molecule.createMolTopol()
  File "/home/jolly/miniconda3/lib/python3.10/site-packages/acpype/topol.py", line 1117, in createMolTopol
    self.molTopol = MolTopol(
  File "/home/jolly/miniconda3/lib/python3.10/site-packages/acpype/topol.py", line 3421, in __init__
    self.xyzFileData = open(acFileXyz).readlines()
FileNotFoundError: [Errno 2] No such file or directory: 'MIN_AC.inpcrd'
Total time of execution: 1s

jollydai

sobereva 发表于 2023-6-28 18:28
有机小分子改用的是GAFF而非AMBER力场，看http://sobereva.com/soft/Sobtop/#FAQ2了解力场之间的关系
如今 ...

太好了！非常感谢！

sobereva

有机小分子改用的是GAFF而非AMBER力场，看http://sobereva.com/soft/Sobtop/#FAQ2了解力场之间的关系
如今一律推荐用sobtop（http://sobereva.com/soft/Sobtop）生成拓扑文件，比acpype灵活好用得多，没那么多破毛病，还不需要装ambertools、不需要非得linux环境