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标题: 关于acpype.py生成拓扑文件报错，无诡异的成键 [打印本页]

作者
Author: zwn 时间: 2021-9-8 20:21
标题: 关于acpype.py生成拓扑文件报错，无诡异的成键
各位老师，之前我在群里问过类似的问题，但是没有解决，现传上mol2文件。问题如下：
1.我用B3LYP优化好分子，然后用gview修改了诡异的成键方式，另存为mol2文件，用acpype生成拓扑文件时，报错如下：

[root@localhost 1212121]# ./acpype.py -i TT_2_B3LYP.mol2 -d
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2021 AWSdS |
============================================================================
DEBUG: Python Version 2.7.5
DEBUG: Max execution time tolerance is 10h
WARNING: no 'babel' executable, no PDB file as input can be used!
DEBUG: /root/SoftWare/amber18/bin/antechamber -i TT_2_B3LYP.mol2 -fi mol2 -o tmp -fo ac -pf y
DEBUG:
Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Warning: The number of bonds (4) for atom (ID: 23, Name: C23) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 26, Name: C26) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 29, Name: C29) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 32, Name: C32) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 35, Name: C35) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 39, Name: C39) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 41, Name: C41) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 44, Name: C44) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 47, Name: C47) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 49, Name: C49) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 52, Name: C52) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 54, Name: C54) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 57, Name: C57) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 60, Name: C60) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 63, Name: C63) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 66, Name: C66) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 70, Name: C70) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 73, Name: C73) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 75, Name: C75) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 78, Name: C78) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 82, Name: C82) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 84, Name: C84) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
But, you may safely ignore the warnings if your molecule
      uses atom names or element names as atom types.
-- Check Geometry --
   for those bonded
   for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.

Warning: The assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
(be cautious, using a large value of PSCUTOFF (>100) will
significantly increase the computation time).

DEBUG: setResNameCheckCoords done
DEBUG: Net charge drift '0.000000'
==> ... charge set to 0
==> Executing Antechamber...
==> Debugging...
DEBUG: /root/SoftWare/amber18/bin/antechamber -i TT_2_B3LYP.mol2 -fi mol2 -o TT_2_B3LYP_bcc_gaff.mol2 -fo mol2 -c bcc -nc 0 -m 1 -s 2 -df 2 -at gaff -pf n
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
Status: pass
Info: Finished reading file (TT_2_B3LYP.mol2).
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Warning: The number of bonds (4) for atom (ID: 23, Name: C23) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 26, Name: C26) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 29, Name: C29) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 32, Name: C32) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 35, Name: C35) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 39, Name: C39) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 41, Name: C41) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 44, Name: C44) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 47, Name: C47) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 49, Name: C49) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 52, Name: C52) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 54, Name: C54) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 57, Name: C57) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 60, Name: C60) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 63, Name: C63) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 66, Name: C66) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 70, Name: C70) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 73, Name: C73) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 75, Name: C75) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 78, Name: C78) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 82, Name: C82) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 84, Name: C84) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
But, you may safely ignore the warnings if your molecule
      uses atom names or element names as atom types.
-- Check Geometry --
   for those bonded
   for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.

Running: /root/SoftWare/amber18/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Warning: The assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
(be cautious, using a large value of PSCUTOFF (>100) will
significantly increase the computation time).

Running: /root/SoftWare/amber18/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 309; net charge: 0
Info: The number of electrons is odd (309).
   Please check the total charge (-nc flag) and spin multiplicity (-m flag).

Running: /root/SoftWare/amber18/bin/sqm -O -i sqm.in -o sqm.out
/root/SoftWare/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/root/SoftWare/amber18/bin/sqm -O -i sqm.in -o sqm.out".

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
DEBUG: /root/SoftWare/amber18/bin/parmchk2 -i TT_2_B3LYP_bcc_gaff.mol2 -f mol2 -o TT_2_B3LYP_AC.frcmod
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Cannot open file (TT_2_B3LYP_bcc_gaff.mol2) with mode (r).
No such file or directory
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
ACPYPE FAILED: [Errno 2] No such file or directory: 'TT_2_B3LYP_AC.prmtop'
  File "./acpype.py", line 3569, in <module>
molecule.createMolTopol()
  File "./acpype.py", line 1241, in createMolTopol
self.topFileData = open(self.acTopFileName, 'r').readlines()
Total time of execution: less than a second
[root@localhost 1212121]#

2.我又尝试用obabel 和 antechamber 转mol2之后，acpype也都报错，其中，antechamber生成的mol2文件进行acpype报错如下：
[root@localhost 1212121]# ./acpype.py -i TT2A.mol2 -d
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2021 AWSdS |
============================================================================
DEBUG: Python Version 2.7.5
DEBUG: Max execution time tolerance is 10h
WARNING: no 'babel' executable, no PDB file as input can be used!
DEBUG: /root/SoftWare/amber18/bin/antechamber -i TT2A.mol2 -fi mol2 -o tmp -fo ac -pf y
DEBUG:
Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
   for those bonded
   for those not bonded
Status: pass
-- Check Weird Bonds --
/root/SoftWare/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (3) for atom (ID: 1, Name: C).
   Possible open valence.
ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'
  File "./acpype.py", line 3558, in <module>
is_sorted=options.sorted, chiral=options.chiral)
  File "./acpype.py", line 3155, in __init__
self.setResNameCheckCoords()
  File "./acpype.py", line 673, in setResNameCheckCoords
tmpFile = open('tmp', 'r')
Total time of execution: less than a second
[root@localhost 1212121]#

请问这是怎么回事？antechamber是严格按照卢老师课上讲的编译的，生成其他拓扑文件都没有报过错。

作者
Author: sun666 时间: 2021-9-8 23:23
是不是有芳香环

作者
Author: sobereva 时间: 2021-9-9 01:17
C76明显少氢
(, 下载次数 Times of downloads: 35)

作者
Author: zwn 时间: 2021-9-9 08:53
本帖最后由 zwn 于 2021-9-9 08:54 编辑

sobereva 发表于 2021-9-9 01:17
C76明显少氢

sob老师，将C76改成一个双键，定义成sp2的碳，也是报错如下：
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2021 AWSdS |
============================================================================
DEBUG: Python Version 2.7.5
DEBUG: Max execution time tolerance is 10h
WARNING: no 'babel' executable, no PDB file as input can be used!
DEBUG: /root/SoftWare/amber18/bin/antechamber -i TT_3_B3LYP.mol2 -fi mol2 -o tmp -fo ac -pf y
DEBUG:
Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Warning: The number of bonds (2) for atom (ID: 24, Name: N24) does not match
      the connectivity (3) for atom type (N) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 25, Name: C25) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 28, Name: C28) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 30, Name: C30) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 32, Name: C32) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 35, Name: C35) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 38, Name: C38) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 41, Name: C41) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 44, Name: C44) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 47, Name: C47) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 50, Name: C50) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 53, Name: C53) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 57, Name: C57) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 60, Name: C60) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 63, Name: C63) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 66, Name: C66) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 76, Name: C76) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 78, Name: C78) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 81, Name: C81) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 84, Name: C84) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 86, Name: C86) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 90, Name: C90) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 93, Name: C93) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 96, Name: C96) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 99, Name: C99) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 104, Name: C104) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 106, Name: C106) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 108, Name: C108) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 112, Name: O112) does not match
      the connectivity (1) for atom type (O) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 115, Name: C115) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 118, Name: C118) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 120, Name: C120) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 124, Name: C124) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 127, Name: C127) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 132, Name: C132) does not match
      the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
But, you may safely ignore the warnings if your molecule
      uses atom names or element names as atom types.

作者
Author: zwn 时间: 2021-9-9 09:02

sun666 发表于 2021-9-8 23:23
是不是有芳香环

是的，稠环体系

作者
Author: sobereva 时间: 2021-9-10 02:20

zwn 发表于 2021-9-9 08:53
sob老师，将C76改成一个双键，定义成sp2的碳，也是报错如下：
| ACPYPE: AnteChamber PYthon Parser int ...

少氢又不是改成双键能解决的，完全是两码事

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