使用acpype对UCSF Chimera处理后结构进行计算，有时会出现Errno2，利用acpype -di ***.mol2 -c user

可以得到更详细的报错信息，如下：

=================================================================================================

| ACPYPE: AnteChamber PYthon Parser interfacE v. 2017-01-17 22:13:52Z Rev: 10101 (c) 2017 AWSdS |

=================================================================================================

DEBUG: Python Version 2.7.6

DEBUG: Max execution time tolerance is 10h

WARNING: no 'babel' executable, no PDB file as input can be used!

DEBUG: /home/wu3857/Softwares/amber16/bin/antechamber -i UNN.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 --

/home/wu3857/Softwares/amber16/bin/to_be_dispatched/antechamber: Fatal Error!

Weird atomic valence (5) for atom (ID: 17, Name: C12).

       Possible open valence.

ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'

  File "/usr/local/bin/acpype", line 3558, in

    is_sorted=options.sorted, chiral=options.chiral)

  File "/usr/local/bin/acpype", line 3155, in __init__

    self.setResNameCheckCoords()

  File "/usr/local/bin/acpype", line 673, in setResNameCheckCoords

    tmpFile = open('tmp', 'r')

Total time of execution: less than a second

 

可以注意到具体问题出现在红字部分，无法对所输入文件的第17号原子的电价进行平衡，回到mol2文件中查看

@MOLECULE

CID_3pe3_1.pdb

58 63 1 0 0

LARGE

AMBER ff99SB

@ATOM

      1 O          -3.1250  207.1180   32.0170 O.3       1 UNN   -0.2172

      2 O          -2.3330  211.7900   31.6550 O.3       1 UNN   -0.2242

      3 O          -4.0420  210.4680   30.2570 O.2       1 UNN   -0.5741

      4 O          -3.5130  215.1260   33.3660 O.2       1 UNN   -0.5901

      5 C          -3.5660  209.4110   32.1820 C.2       1 UNN   -0.1962

      6 C          -3.8970  210.5390   32.8590 C.ar      1 UNN   -0.1848

      7 C          -3.3640  211.7510   32.5560 C.ar      1 UNN    0.2351

      8 C          -3.1910  208.2490   32.7820 C.2       1 UNN    0.2359

      9 C          -3.7750  212.8650   33.2050 C.ar      1 UNN   -0.3356

     10 C          -3.5790  209.4850   30.8070 C.2       1 UNN    0.5877

     11 C          -3.1080  208.4400   30.0620 C.ar      1 UNN   -0.3386

     12 C          -4.8130  210.4370   33.8440 C.ar      1 UNN    0.2391

     13 C          -2.8540  207.2820   30.6980 C.ar      1 UNN    0.2051

     14 C          -4.7110  212.7770   34.1790 C.ar      1 UNN    0.2651

     15 C          -2.8630  208.0940   34.0970 C.ar      1 UNN   -0.1318

     16 C          -5.2000  211.5590   34.4620 C.ar      1 UNN   -0.2420

     17 C          -3.2270  214.0660   32.8460 C.2       1 UNN    0.5877

     18 C          -1.9000  212.9930   31.1900 C.2       1 UNN    0.2069

……

@BOND

     1    1    8 1

     2    1   13 1

     3    2    7 1

     4    2   18 1

     5    3   10 2

     6    4   17 2

     7    5    6 1

     8    5    8 2

     9    5   10 1

    10    6    7 ar

    11    6   12 ar

    12    7    9 ar

    13    8   15 1

    14    9   14 ar

    15    9   17 1

    16   10   11 1

    17   11   13 ar

    18   11   19 ar

    19   12   16 ar

    20   12   29 1

    21   13   21 ar

    22   14   16 ar

    23   14   41 1

    24   15   24 ar

    25   15   25 ar

    26   17   20 2

    27   18   20 2

    28   18   33 1

……

 

该结构如下图，17号C为红圈中。

http://s12/bmiddle/001ZFeMBzy7h7y88b9Ncb&6902的解决方法" />

不论如何C所能形成的化学键上限为4。在mol2文件对各原子的化学键进行了详细定义：首列为bond序号，其

次是2个原子序号，最后是bond的类型，即1、2、3键及苯环等不同的键类型。

http://s2/bmiddle/001ZFeMBzy7h7y50JdT61&690

回到上面的mol2文件中，会发现17号原子所成键数量为2+1+2=5，明显与最基本的化学性质相悖，且该位置

并没有携带额外的电荷，因此出现Weird atomic valence (5) for atom (ID: 17, Name: C12)这样的报错。

 

按照具体的成键情况将错误的键修改后再运行，可以成功。

=================================================================================================

| ACPYPE: AnteChamber PYthon Parser interfacE v. 2017-01-17 22:13:52Z Rev: 10101 (c) 2017 AWSdS |

=================================================================================================

DEBUG: Python Version 2.7.6

DEBUG: Max execution time tolerance is 10h

WARNING: no 'babel' executable, no PDB file as input can be used!

DEBUG: /home/wu3857/Softwares/amber16/bin/antechamber -i UNN.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 --

   Status: pass

-- Check Number of Units --

   Status: pass

acdoctor mode has completed checking the input file.

DEBUG: setResNameCheckCoords done

==> Reading user's charges from mol2 file...

==> Debugging...

DEBUG: /home/wu3857/Softwares/amber16/bin/antechamber -i UNN.mol2 -fi mol2 -o tmp -fo mol2 -c wc -cf tmp.crg -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

-- Check Unusual Elements --

   Status: pass

-- Check Open Valences --

   Status: pass

-- 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.

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

DEBUG: readMol2TotalCharge: 0.001

DEBUG: Net charge drift '0.001000'

==> ... charge set to 0

==> Executing Antechamber...

==> Debugging...

DEBUG: /home/wu3857/Softwares/amber16/bin/antechamber -i UNN.mol2 -fi mol2 -o UNN_user_gaff.mol2 -fo mol2  -nc 0 -m 1 -s 2 -df 2 -at gaff -pf n

==> * Antechamber OK *

DEBUG: /home/wu3857/Softwares/amber16/bin/parmchk2 -i UNN_user_gaff.mol2 -f mol2 -o UNN_AC.frcmod

==> * Parmchk OK *

==> Executing Tleap...

DEBUG: /home/wu3857/Softwares/amber16/bin/tleap -f tleap.in

++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Checking 'UNN'....

Checking parameters for unit 'UNN'.

Checking for bond parameters.

Checking for angle parameters.

Unit is OK.

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

==> * Tleap OK *

DEBUG: prmtop and inpcrd files loaded

DEBUG: basename defined = 'UNN'

DEBUG: getCoords done

DEBUG: getABCOEFs done

DEBUG: charge to be balanced: total  0.0010000032

DEBUG: balanceCharges done

DEBUG: Balanced TotalCharge -0.0000000000

DEBUG: PBC = None

DEBUG: getAtoms done

DEBUG: getBonds done

DEBUG: getAngles done

DEBUG: getDihedrals done

==> Writing NEW PDB file

==> Writing CNS/XPLOR files

DEBUG: No 'obchiral' to process chiral atoms. Consider installing http://openbabel.org

==> Writing GROMACS files

DEBUG: writing GRO file

DEBUG: Box size estimated

DEBUG: atomTypes 9

DEBUG: GMX atomtypes done

DEBUG: atoms 58

DEBUG: GMX atoms done

DEBUG: bonds 63

DEBUG: GMX bonds done

DEBUG: atomPairs 134

DEBUG: GMX pairs done

DEBUG: angles 98

DEBUG: GMX angles done

DEBUG: setProperDihedralsCoef done

DEBUG: properDihedralsCoefRB 152

DEBUG: properDihedralsAlphaGamma 0

DEBUG: properDihedralsGmx45 152

==> Writing GMX dihedrals for GMX 4.5 and higher.

DEBUG: GMX special proper dihedrals done

DEBUG: improperDihedrals 30

DEBUG: GMX improper dihedrals done

==> Writing CHARMM files

DEBUG: /home/wu3857/Softwares/amber16/bin/antechamber -i UNN_user_gaff.mol2 -fi mol2 -o UNN_CHARMM -fo charmm -s 2 -at gaff  -pf n -rn UNN

==> Writing pickle file UNN.pkl

Total time of execution: 1s