zwn 发表于 2021-9-9 08:53 少氢又不是改成双键能解决的，完全是两码事 |
本帖最后由 zwn 于 2021-9-9 08:54 编辑 sobereva 发表于 2021-9-9 01:17 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. |
C76明显少氢
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| 是不是有芳香环 |
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