acpype出现Errno 2的解决方法
2018-01-04 23:24阅读：
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
D
EBUG:
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。
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。
![计算机生成了可选文字: @<TRI POS> BON D Each data record associated with this RTI consists Of a single data line which contains all the information necessary to reconstruct one bonds in the molecule. Format: bond id orxgxn atom id target atom id bond type [status bits] bond id (integer) =the ID number Of the bond atthe time the file was created. This is provided for reference only and is not used when the ． mo 《 2 file is read into SYBYL origin atom id (integer) = the ID number ofthe atom at one end Of the bond target_atom id (integer) = the ID number ofthe atom atthe Other end Of the bond bond_type (string) = the SYBYL bond type (see below). Status bits (string) the internal SYBYL Status bits associated with the bond. e 丷 should e](http://s2.sinaimg.cn/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
