gpu加速版acpype运行错误

gaosimeng2001

我用十二烷基苯磺酸钠试算发现acpype脚本运行不了，求各位老师指教


./acpype.py -i C12-ph-so3-1.mol2        -n -1
===============================================================       =============
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c)        2019 AWSdS |
===============================================================       =============
WARNING: no 'babel' executable, no PDB file as input can be use       d!
==> ... charge set to -1
==> Executing Antechamber...
==> AC output file present... doing nothing
==> * Antechamber OK *
++++++++++start_quote++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++
/bin/sh: -c:行0: 未预期的符号 `(' 附近有语法错误
/bin/sh: -c:行0: `which: no parmchk in (/sob/amber18/bin:/sob/g       mx2018.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:       /home/gsm/soft/openmpi:/home/gsm/soft/g09:/sob/packmol-18.169:/       home/gsm/.local/bin:/home/gsm/bin) -i C12-ph-so3-1_bcc_gaff.mol       2 -f mol2 -o C12-ph-so3-1_AC.frcmod'
++++++++++end_quote++++++++++++++++++++++++++++++++++++++++++++       +++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'C12-ph-so3       -1_AC.prmtop'
Total time of execution: less than a second


坐标文件中的Ar已经更换成ar了，求教这个提示是啥意思?如何解决？

sobereva

不要用那么大的字号，给你改了。若无特殊情况， 字号一律用论坛默认的字号
acpype没有所谓的GPU版

8成是你amber没配置好。先确保直接输入antechamber能启动相应程序。说不清楚的话直接把mol2文件上传

gaosimeng2001

sobereva 发表于 2019-7-24 14:11
不要用那么大的字号，给你改了。若无特殊情况， 字号一律用论坛默认的字号
acpype没有所谓的GPU版

输入antechamber后提示：
[gsm@localhost C12-ph-so3na]$ antechamber

Welcome to antechamber 17.3: molecular input file processor.

Usage: antechamber -i   input file name
                   -fi  input file format
                   -o   output file name
                   -fo  output file format
                   -c   charge method
                   -cf  charge file name
                   -nc  net molecular charge (int)
                   -a   additional file name
                   -fa  additional file format
                   -ao  additional file operation
                        crd   : only read in coordinate
                        crg   : only read in charge
                        radius: only read in radius
                        name  : only read in atom name
                        type  : only read in atom type
                        bond  : only read in bond type
                   -m   multiplicity (2S+1), default is 1
                   -rn  residue name, overrides input file, default is MOL
                   -rf  residue toplogy file name in prep input file,
                        default is molecule.res
                   -ch  check file name for gaussian, default is 'molecule'
                   -ek  mopac or sqm keyword, inside quotes; overwrites previous                     ones
                   -gk  gaussian job keyword, inside quotes
                   -gm  gaussian memory keyword, inside quotes, such as "%mem=10                    00MB"
                   -gn  gaussian number of processors keyword, inside quotes, su                    ch as "%nproc=8"
                   -gv  add keyword to generate gesp file (for Gaussian 09 only)
                        1    : yes
                        0    : no, the default
                   -ge  gaussian esp file generated by iop(6/50=1), default is g                    09.gesp
                   -df  am1-bcc precharge flag, 2 - use sqm(default); 0 - use mo                    pac
                   -at  atom type
                        gaff : the default
                        gaff2: for gaff2 (beta-version)
                        amber: for PARM94/99/99SB
                        bcc  : bcc
                        sybyl: sybyl
                   -du  fix duplicate atom names: yes(y)[default] or no(n)
                   -bk  component/block Id, for ccif
                   -an  adjust atom names: yes(y) or no(n)
                        the default is 'y' for 'mol2' and 'ac' and 'n' for the o                    ther formats
                   -j   atom type and bond type prediction index, default is 4
                        0    : no assignment
                        1    : atom type
                        2    : full  bond types
                        3    : part  bond types
                        4    : atom and full bond type
                        5    : atom and part bond type
                   -s   status information: 0(brief), 1(default) or 2(verbose)
                   -eq  equalizing atomic charge, default is 1 for '-c resp' and                     '-c bcc' and 0 for the other charge methods
                        0    : no use
                        1    : by atomic paths
                        2    : by atomic paths and structural information, i.e.                     E/Z configurations
                   -pf  remove intermediate files: yes(y) or no(n)[default]
                   -pl  maximum path length to determin equivalence of atomic ch                    arges for resp and bcc,
                        the smaller the value, the faster the algorithm, default                     is -1 (use full length),
                        set this parameter to 10 to 30 if your molecule is big (                    # atoms >= 100)
                   -dr  acdoctor mode: yes(y)[default] or no(n)
                   -i -o -fi and -fo must appear; others are optional
                   Use 'antechamber -L' to list the supported file formats and c                    harge methods

sobereva

用我把Ar改为ar后的mol2文件能正常处理：
x.mol2 (2.85 KB, 下载次数 Times of downloads: 48)

2019-7-24 15:25 上传 Uploaded

点击下载
Click to download

如果你是之前参加过科音动力学培训班的学员，我这里用的操作系统、acpype、Amber都是和培训里一样，安装方式也都和课上说的一样

[root@192 other]# ./acpype.py -i x.mol2 -n -1
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2019 AWSdS |
============================================================================
==> ... charge set to -1
==> Executing Antechamber...
==> * Antechamber OK *
==> * Parmchk OK *
==> Executing Tleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Checking 'MOL'....

/sob/amber18/bin/teLeap: Warning!
The unperturbed charge of the unit (-0.999999) is not zero.
Checking parameters for unit 'MOL'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 1
Unit is OK.
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
==> * Tleap OK *
==> Removing temporary files...
==> Writing NEW PDB file

==> Writing CNS/XPLOR files

==> Writing GROMACS files

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

==> Writing CHARMM files

==> Writing pickle file x.pkl
Total time of execution: 2m 3s

gaosimeng2001

sobereva 发表于 2019-7-24 15:25
用我把Ar改为ar后的mol2文件能正常处理：

卢老师，我用acpype运行的时候把Ar改成ar了，给您发的文件里确实没有改，我用的是gpu加速的cuda版本，用普通未加速的是可以正常运行的，安装所有程序的过程都是按照您培训给的视频操作的。

gaosimeng2001

sobereva 发表于 2019-7-24 15:25
用我把Ar改为ar后的mol2文件能正常处理：

下面是我运行x.mol文件的提示

[gsm@localhost C18-so4na]$ ./acpype.py -i x.mol2 -n -1
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2019 AWSdS |
============================================================================
WARNING: no 'babel' executable, no PDB file as input can be used!
==> ... charge set to -1
==> Executing Antechamber...
==> * Antechamber OK *
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/bin/sh: -c:行0: 未预期的符号 `(' 附近有语法错误
/bin/sh: -c:行0: `which: no parmchk in (/sob/amber18/bin:/sob/gmx2018.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/gsm/soft/openmpi:/home/gsm/soft/g09:/sob/packmol-18.169:/home/gsm/.local/bin:/home/gsm/bin) -i x_bcc_gaff.mol2 -f mol2 -o x_AC.frcmod'
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'x_AC.prmtop'
Total time of execution: 55s

sobereva

严格按照课上的步骤，重新装一遍ambertools18再试

这是我的acpype，也尝试这个
acpype.py (143.36 KB, 下载次数 Times of downloads: 213)

2019-7-24 16:37 上传 Uploaded

点击下载
Click to download

yuclark

请问一下，我的中性分子是可以执行的
[root@localhost tf2n]# ./acpype.py -i h2o-1.mol2
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2019 AWSdS |
============================================================================
WARNING: no 'babel' executable, no PDB file as input can be used!
==> ... charge set to 0
==> Executing Antechamber...
==> AC output file present... doing nothing
==> * Antechamber OK *
==> * Parmchk OK *
==> Topologies files already present... doing nothing
==> * Tleap OK *
==> Removing temporary files...
==> Writing NEW PDB file

==> Writing CNS/XPLOR files

==> Writing GROMACS files

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

==> Writing CHARMM files

==> Pickle file h2o-1.pkl already present... doing nothing
Total time of execution: less than a second
当我换成带电荷的时候就会有错误如下所示，不知道怎么解决（而且我重新装了ambertools18）
[root@localhost tf2n]# ./acpype.py -i tf2n.mol2 -n -1
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2019 AWSdS |
============================================================================
WARNING: no 'babel' executable, no PDB file as input can be used!
ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'
Total time of execution: less than a second

yuclark

这是mol2文件

sobereva

加上-d就知道怎么回事
此体系成键方式太特殊，搞不了

yuclark

老师，这是计算阴离子时候的报错信息,如下所示：（计算中性分子个阳离子时不会出错），您看有什么办法可以解决呢？

[root@localhost tf2n]# ./acpype.py -i tf2n.mol2  -d
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2019 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: /sob/amber18/bin/antechamber -i tf2n.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: 1, Name: S1) does not match
         the connectivity (2) for atom type (S) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 4, Name: S4) does not match
         the connectivity (2) for atom type (S) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 7, Name: N7) 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: 8, Name: C8) 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: 9, Name: C9) 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 --
/sob/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (2) for atom (ID: 7, Name: N7).
       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

songyidan

老师您好，我使用了您的脚本，但是在服务器运行的时候出现“ No such file or directory: 'tmp'”报错。
请问是否是脚本中默认在虚拟机中运行所以才是 /tmp/吗，如果想在服务器上使用，我应该如何改脚本呢？

wind

songyidan 发表于 2021-4-8 22:15
老师您好，我使用了您的脚本，但是在服务器运行的时候出现“ No such file or directory: 'tmp'”报错。
...

您好，请问找到解决的办法了嘛

sobereva

songyidan 发表于 2021-4-8 22:15
老师您好，我使用了您的脚本，但是在服务器运行的时候出现“ No such file or directory: 'tmp'”报错。
...

和是不是虚拟机无关
这种报错大多是acpype没能正常运行完毕所致，加上-d从报错输出试图判断原因