How to install and run ACPYPE on Linux?

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

The ACPYPE server is down, so I want to install it on my own Linux (Win10 subsystem). I install the AmberTools21 and pip install acpype

When running ACPYPE, I got error:

Running: /home/username/miniconda3/envs/AmberTools21/bin/mopac.sh
sh: 1: /home/username/miniconda3/envs/AmberTools21/bin/mopac.sh: not found
/home/username/miniconda3/envs/AmberTools21/bin/wrapped_progs/antechamber: Fatal Error!
Cannot properly run "/home/username/miniconda3/envs/AmberTools21/bin/mopac.sh".

It seems that mopac is no longer supported as shown here.

So can we really run ACPYPE on our own Linux?

2

This question is not related to GROMACS; try the AMBER mailing list.

3

sure, I will do that.

4

Dear Ianselibai,
After have installed ambertools, insert the following line:
/home/username/miniconda3/envs/AmberTools21/amber.sh
in file .bashrc in your home directory (I’m not sure if amber.sh script will be in this folder, please check it location).
You can, alternatively, download and install a standalone Ambertools suite from AmberTools21.
If you have access to Gaussian09 (or Gaussian16) and if you like RESP charges (which is considered better charge model than bcc), you can do the following:

  1. Optimize the geometry of your molecule using, for exemple, B3Lyp/cc-pvdz:
    #P opt b3lyp/cc-pvdz geom=connectivity
  2. Calculate MK charges of the optimized molecule using:
    #P b3lyp/cc-pvdz geom=connectivity iop(6/33=2,6/41=10,6/42=17) pop=mk
  3. Calculate RESP charges and produce Triplos mol2 file using:
    antechamber -fi gout -fo mol2 -i molecule.log -o molecule.mol2 -c resp -rn MOL
    (change molecule and MOL as you wish!)
  4. create topologies files for gromacs (for GAFF, OPLS, charmm or CNS force fields) using:
    acpype -i molecule.mol2 -n X -c user
    where X is the charge of your molecule (it is not necessary for nonionic molecules).
    That’s all!
5

Dear parpires,

When I am installing ACPYPE on another WSL (Win10 subsystem Linux), I cannot install openbabel:
sudo apt-get install openbabel

I got error message:

Setting up libc-bin (2.31-0ubuntu9.2) ...
Aborted (core dumped)
/sbin/ldconfig.real: Can't stat /usr/local/lib/x86_64-linux-gnu: No such file or directory
/sbin/ldconfig.real: Path `/usr/lib/x86_64-linux-gnu' given more than once
/sbin/ldconfig.real: Path `/lib/x86_64-linux-gnu' given more than once
/sbin/ldconfig.real: Path `/usr/lib/x86_64-linux-gnu' given more than once
/sbin/ldconfig.real: Path `/usr/lib' given more than once
/usr/lib/x86_64-linux-gnu/libfakeroot:
        libfakeroot-0.so -> libfakeroot-tcp.so
/usr/local/lib:
/lib/x86_64-linux-gnu:
Aborted (core dumped)
dpkg: error processing package libc-bin (--configure):
 installed libc-bin package post-installation script subprocess returned error exit status 134
Errors were encountered while processing:
 libc-bin
E: Sub-process /usr/bin/dpkg returned an error code (1)

There are many questions and solutions about libc-bin, e.g. here, but this could not solve on my WSL.

6

Sorry Ianselibai,
I don’t have any experience in using WSL, but I believe that Microsoft did a lot of modifications in their (I mean, the ones present in Microsoft Store) linux distributions to make them work inside Windows 10.
Why don’t you try to install openbabel from the source? You can download it from Category:Installation - Open Babel
Good luck.

Paulo A.

7

Thank you Paulo.

Now I have downloaded the source file openbabel-3.1.1-source.tar.bz2 from here. Then compile it based on here.

sudo apt-get install openbabel
tells me
openbabel is already the newest version (3.0.0+dfsg-3ubuntu3)

However,
acpype -i xxx.pdb
tells me
ERROR: no 'babel' executable; you need it if input is PDB

8

I remember having similar issues when installing ACPYPE.

What does babel --version return? I’ve got 2.3.2 installed and ACPYPE is working fine.

9

I got openbabel installed, not babel. This is what I got:

$ babel --version

Command 'babel' not found, did you mean:

  command 'babeld' from deb babeld (1.9.1-1)
  command 'obabel' from deb openbabel (3.0.0+dfsg-3ubuntu3)

Try: sudo apt install <deb name>
10

Dear lanselibai,
do you know where did you installed the obabel executables? If you installed openbabel using the default options, then obabel will be in /usr/local/bin.
To help you find the program, type at the command prompt:
sudo find / -name obabel -print
If you have to many output, type:
sudo find / -name obabel -print >> find.log
and look at find.log to see the directory where obabel is located.
Once you find the obabel location, see if this directory is present in PATH enviroment variable by typing:
echo $PATH
if the obabel directory is not in PATH, edit (as root) the file /etc/profile and type at the end of that file:
export PATH="/obabel/folder:$PATH"
replacing /obabel/folder with the directory where the obabel program is located.
Save the file and type at command prompt:
source /etc/profile
Go to the directory where the obabel program is located:
cd /obabel/folder
(remember to replace /obabel/folder with the correct obabel directory name)
Type the following command to create a symbolic link (aka symlink):
sudo ln -s obabel babel
return to your home folder by typing cd and try to run acpype -i xxx.pdb again.
I hope it will work now! ;-)
Good luck.

Paulo A.

11

Hi Paulo, thank you very much for your detailed step-by-step instruction! Very much appreciated! Your solution can partially work, the babel can be invoked now, but there seems to be a conversion problem. The same PDB can be successfully submitted on the Acpype server, so I think it is not the problem of the PDB file.


============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2021 AWSdS |
============================================================================
==> ... charge set to 0
WARNING: Old version of antechamber. Strongly consider upgrading to AmberTools
WARNING: Setting mopac for antechamber
==> ... converting pdb input file to mol2 input file
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
@<TRIPOS>MOLECULE
EPE.pdb
 33 33 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
      1  N1        -0.8200   -0.3300    0.2580 N.3     1  EPE1       -0.2984
      2  C2        -1.6690    0.5570    1.0610 C.3     1  EPE1        0.0118
      3  C3        -1.6930    0.0720    2.5110 C.3     1  EPE1        0.0118
      4  N4        -0.3420    0.1470    3.0790 N.3     1  EPE1       -0.2977
      5  C5         0.5070   -0.7400    2.2760 C.3     1  EPE1        0.0118
      6  C6         0.5310   -0.2550    0.8260 C.3     1  EPE1        0.0118
      7  C7        -0.4160   -0.4410    4.4230 C.3     1  EPE1        0.0222
      8  C8         0.9660   -0.3950    5.0760 C.3     1  EPE1        0.0569
      9  O8         1.4020    0.9610    5.1740 O.3     1  EPE1       -0.3937
     10  C9        -0.7460    0.2580   -1.0850 C.3     1  EPE1        0.0188
     11  C10        0.1280   -0.6210   -1.9800 C.3     1  EPE1        0.0825
     12  S          0.2190    0.1040   -3.6400 S.3     1  EPE1       -0.0196
     13  O1S       -1.0190   -0.0010   -4.3270 O.3     1  EPE1       -0.0727
     14  O2S        0.9860    1.3010   -3.6460 O.3     1  EPE1       -0.0727
     15  O3S        1.1100   -0.8700   -4.3970 O.3     1  EPE1       -0.2716
     16  H21       -2.6830    0.5510    0.6590 H       1  EPE1        0.0439
     17  H22       -1.2710    1.5710    1.0240 H       1  EPE1        0.0439
     18  H31       -2.0440   -0.9590    2.5430 H       1  EPE1        0.0439
     19  H32       -2.3670    0.7020    3.0930 H       1  EPE1        0.0439
     20  H51        1.5200   -0.7340    2.6770 H       1  EPE1        0.0439
     21  H52        0.1090   -1.7540    2.3130 H       1  EPE1        0.0439
     22  H61        1.2040   -0.8850    0.2440 H       1  EPE1        0.0439
     23  H62        0.8810    0.7750    0.7940 H       1  EPE1        0.0439
     24  H71       -0.7480   -1.4760    4.3480 H       1  EPE1        0.0449
     25  H72       -1.1230    0.1240    5.0290 H       1  EPE1        0.0449
     26  H81        1.6730   -0.9610    4.4700 H       1  EPE1        0.0570
     27  H82        0.9110   -0.8320    6.0730 H       1  EPE1        0.0570
     28  HO8        2.2750    0.9450    5.5900 H       1  EPE1        0.2095
     29  H91       -1.7480    0.3230   -1.5090 H       1  EPE1        0.0443
     30  H92       -0.3130    1.2560   -1.0220 H       1  EPE1        0.0443
     31 H101        1.1310   -0.6870   -1.5570 H       1  EPE1        0.0517
     32 H102       -0.3040   -1.6200   -2.0440 H       1  EPE1        0.0517
     33 HOS3        1.1940   -0.5290   -5.2980 H       1  EPE1        0.2426
@<TRIPOS>BOND
     1     1     2    1
     2     1     6    1
     3     1    10    1
     4     2     3    1
     5     2    16    1
     6     2    17    1
     7     3     4    1
     8     3    18    1
     9     3    19    1
    10     4     5    1
    11     4     7    1
    12     5     6    1
    13     5    20    1
    14     5    21    1
    15     6    22    1
    16     6    23    1
    17     7     8    1
    18     7    24    1
    19     7    25    1
    20     8     9    1
    21     8    26    1
    22     8    27    1
    23     9    28    1
    24    10    11    1
    25    10    29    1
    26    10    30    1
    27    11    12    1
    28    11    31    1
    29    11    32    1
    30    12    13    1
    31    12    14    1
    32    12    15    1
    33    15    33    1
==============================
*** Open Babel Error  in OpenAndSetFormat
  Cannot open EPE.mol2
1 molecule converted
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: convert pdb to mol2 via babel failed
ERROR: convertPdbToMol2 failed
==> Executing Antechamber...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Welcome to antechamber 21.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
/home/lanselibai/miniconda3/envs/AmberTools21/bin/wrapped_progs/antechamber: Fatal Error!
Cannot open the input file (EPE.mol2).
No such file or directory

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/bin/sh: 1: -i: not found
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
==> ... trying Sleap
==> Executing Sleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/bin/sh: 1: -f: not found

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'EPE_AC.prmtop'
Total time of execution: less than a second
12

Dear lanselibai,
Maybe it’s a problem with babel. Try running it like this:
babel -i pdb XXX.pdb -o mol2 XXX.mol2
If it works, you can try using XXX.mol2 with acpype like this:
acpype -i XXX.mol2

Paulo A.

13

Dear Paulo A.

It does not work as well.

$ babel -i EPE.pdb -o mol2 EPE.mol2
babel: cannot read input format!
Open Babel 3.1.0 -- Jun  7 2021 -- 21:58:06
Usage:
babel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]
Try  -H option for more information.

Then I tried the help, I got

$ babel -H
Open Babel converts chemical structures from one file format to another

Usage:
babel[-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]
The extension of a file decides the format, unless it is overridden
 by -i or -o options, e.g. -icml, or -o smi
See below for available format-types, which are the same as the
file extensions and are case independent.
If no input or output file is given stdin or stdout are used instead.

More than one input file can be specified and their names can contain
wildcard chars (* and ?). The format of each file can be different unless
the -i option has been used, when they are all the same.
By default, the molecules are aggregated in the output file,
 but see -m option, Splitting, below.

Options, other than -i -o -O -m, must come after the input files.

Conversion options
-f <#> Start import at molecule # specified
-l <#> End import at molecule # specified
-e Continue with next object after error, if possible
-z Compress the output with gzip
-zin Decompress the input with gzip
-k Attempt to translate keywords
-H Outputs this help text
-Hxxx (xxx is file format ID e.g. -Hcml) gives format info
-Hall Outputs details of all formats
-V Outputs version number
-L <category> Lists plugin classes of this category, e.g. <formats>
   Use just -L for a list of plugin categories.
   Use -L <ID> e.g. -L sdf for details of a format or other plugin.
-m Produces multiple output files, to allow:
    Splitting: e.g.        babel infile.mol -O new.smi -m
      puts each molecule into new1.smi new2.smi etc
    Batch conversion: e.g. babel *.mol -osmi -m
      converts each input file to a .smi file
Interface to OBAPI internals
API options, e.g. ---errorlevel 2
 errorlevel # min warning level displayed

To see a list of recognized file formats use
  babel -L formats [read] [write]
To see details and specific options for a particular format, e.g CML, use
  babel -L cml
14

Dear Ianselibai,
the correct syntax of Babel is:
babel -i pdb EPE.pdb -o mol2 EPE.mol2
You forgot the pdb after -i and before EPE.pdb.
And remember: Linux is case sensitive. Make sure that the filename is EPE.pdb, not epe.pdb.

Paulo A.

15

Dear Paulo, thank you!

I got this error below and there is nothing generated in the working folder

$ babel -i pdb EPE.pdb -o mol2 EPE.mol2
@<TRIPOS>MOLECULE
EPE.pdb
 33 33 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
      1  N1        -0.8200   -0.3300    0.2580 N.3     1  EPE1       -0.2984
      2  C2        -1.6690    0.5570    1.0610 C.3     1  EPE1        0.0118
      3  C3        -1.6930    0.0720    2.5110 C.3     1  EPE1        0.0118
      4  N4        -0.3420    0.1470    3.0790 N.3     1  EPE1       -0.2977
      5  C5         0.5070   -0.7400    2.2760 C.3     1  EPE1        0.0118
      6  C6         0.5310   -0.2550    0.8260 C.3     1  EPE1        0.0118
      7  C7        -0.4160   -0.4410    4.4230 C.3     1  EPE1        0.0222
      8  C8         0.9660   -0.3950    5.0760 C.3     1  EPE1        0.0569
      9  O8         1.4020    0.9610    5.1740 O.3     1  EPE1       -0.3937
     10  C9        -0.7460    0.2580   -1.0850 C.3     1  EPE1        0.0188
     11  C10        0.1280   -0.6210   -1.9800 C.3     1  EPE1        0.0825
     12  S          0.2190    0.1040   -3.6400 S.3     1  EPE1       -0.0196
     13  O1S       -1.0190   -0.0010   -4.3270 O.3     1  EPE1       -0.0727
     14  O2S        0.9860    1.3010   -3.6460 O.3     1  EPE1       -0.0727
     15  O3S        1.1100   -0.8700   -4.3970 O.3     1  EPE1       -0.2716
     16  H21       -2.6830    0.5510    0.6590 H       1  EPE1        0.0439
     17  H22       -1.2710    1.5710    1.0240 H       1  EPE1        0.0439
     18  H31       -2.0440   -0.9590    2.5430 H       1  EPE1        0.0439
     19  H32       -2.3670    0.7020    3.0930 H       1  EPE1        0.0439
     20  H51        1.5200   -0.7340    2.6770 H       1  EPE1        0.0439
     21  H52        0.1090   -1.7540    2.3130 H       1  EPE1        0.0439
     22  H61        1.2040   -0.8850    0.2440 H       1  EPE1        0.0439
     23  H62        0.8810    0.7750    0.7940 H       1  EPE1        0.0439
     24  H71       -0.7480   -1.4760    4.3480 H       1  EPE1        0.0449
     25  H72       -1.1230    0.1240    5.0290 H       1  EPE1        0.0449
     26  H81        1.6730   -0.9610    4.4700 H       1  EPE1        0.0570
     27  H82        0.9110   -0.8320    6.0730 H       1  EPE1        0.0570
     28  HO8        2.2750    0.9450    5.5900 H       1  EPE1        0.2095
     29  H91       -1.7480    0.3230   -1.5090 H       1  EPE1        0.0443
     30  H92       -0.3130    1.2560   -1.0220 H       1  EPE1        0.0443
     31 H101        1.1310   -0.6870   -1.5570 H       1  EPE1        0.0517
     32 H102       -0.3040   -1.6200   -2.0440 H       1  EPE1        0.0517
     33 HOS3        1.1940   -0.5290   -5.2980 H       1  EPE1        0.2426
@<TRIPOS>BOND
     1     1     2    1
     2     1     6    1
     3     1    10    1
     4     2     3    1
     5     2    16    1
     6     2    17    1
     7     3     4    1
     8     3    18    1
     9     3    19    1
    10     4     5    1
    11     4     7    1
    12     5     6    1
    13     5    20    1
    14     5    21    1
    15     6    22    1
    16     6    23    1
    17     7     8    1
    18     7    24    1
    19     7    25    1
    20     8     9    1
    21     8    26    1
    22     8    27    1
    23     9    28    1
    24    10    11    1
    25    10    29    1
    26    10    30    1
    27    11    12    1
    28    11    31    1
    29    11    32    1
    30    12    13    1
    31    12    14    1
    32    12    15    1
    33    15    33    1
==============================
*** Open Babel Error  in OpenAndSetFormat
  Cannot open EPE.mol2
1 molecule converted
16

Dear Ianselibai,
at least, now, we discover the reason of the error in the acpype:

There are several possible reasons for the error in Babel. It can be, for example, a question of permissions in your work folder (see here, for example: How to Manage File and Folder Permissions in Linux - Linux.com).
Try converting to another file format to see if it works, for example:
babel -i pdb XXX.pdb -o xyz XXX.xyz
Or try to use babel in another folder, if you are having permissions problem, using the following sequence of commands:
mkdir test
cp EPE.pdb test/.
cd test
babel -i pdb EPE.pdb -o mol2 EPE.mol2
To delete test folder do the following:
cd …
rm -rf test

Another possibility is to use antechamber to create the mol2 file from pdb:
antechamber -fi pdb -fo mol2 -i EPE.pdb -o EPE.mol2
(type antechamber -h for help and antechamber -L for a list of file formats it supports)

Paulo A.

17

Thank you for the help.

Converting to xyz format also does not work:

$ babel -i pdb EPE.pdb -o xyz EPE.xyz
33
EPE.pdb
N         -0.82000       -0.33000        0.25800
C         -1.66900        0.55700        1.06100
C         -1.69300        0.07200        2.51100
N         -0.34200        0.14700        3.07900
C          0.50700       -0.74000        2.27600
C          0.53100       -0.25500        0.82600
C         -0.41600       -0.44100        4.42300
C          0.96600       -0.39500        5.07600
O          1.40200        0.96100        5.17400
C         -0.74600        0.25800       -1.08500
C          0.12800       -0.62100       -1.98000
S          0.21900        0.10400       -3.64000
O         -1.01900       -0.00100       -4.32700
O          0.98600        1.30100       -3.64600
O          1.11000       -0.87000       -4.39700
H         -2.68300        0.55100        0.65900
H         -1.27100        1.57100        1.02400
H         -2.04400       -0.95900        2.54300
H         -2.36700        0.70200        3.09300
H          1.52000       -0.73400        2.67700
H          0.10900       -1.75400        2.31300
H          1.20400       -0.88500        0.24400
H          0.88100        0.77500        0.79400
H         -0.74800       -1.47600        4.34800
H         -1.12300        0.12400        5.02900
H          1.67300       -0.96100        4.47000
H          0.91100       -0.83200        6.07300
H          2.27500        0.94500        5.59000
H         -1.74800        0.32300       -1.50900
H         -0.31300        1.25600       -1.02200
H          1.13100       -0.68700       -1.55700
H         -0.30400       -1.62000       -2.04400
H          1.19400       -0.52900       -5.29800
==============================
*** Open Babel Error  in OpenAndSetFormat
  Cannot open EPE.xyz
1 molecule converted

Then I tried making a new folder, copy the pdb, and run the babel again, still the same, not work. So I think I already have the permission for the folders, but the babel does not work.

Then I used the antechamber. Even though the “no version information available” appears in the last two lines, an EPE.mol2 file was generated!

$ antechamber -fi pdb -fo mol2 -i EPE.pdb -o EPE.mol2

Welcome to antechamber 21.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for pdb 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.

/bin/bash: /home/lanselibai/miniconda3/envs/AmberTools21/lib/libtinfo.so.6: no version information available (required by /bin/bash)
/bin/bash: /home/lanselibai/miniconda3/envs/AmberTools21/lib/libtinfo.so.6: no version information available (required by /bin/bash)

So I can now try to use the generated mol2 file for acpype, but got the “mopac.sh: not found” error, which I mentioned in the 1st thread.:

$ acpype -i EPE.mol2
============================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2021 AWSdS |
============================================================================
==> ... charge set to 0
WARNING: Old version of antechamber. Strongly consider upgrading to AmberTools
WARNING: Setting mopac for antechamber
==> Executing Antechamber...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Welcome to antechamber 21.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for mol2 File --
   Status: pass
Info: Ignoring Mol2 record type (@<TRIPOS>SUBSTRUCTURE).
Info: Finished reading file (EPE.mol2); atoms read (33), bonds read (33).
Info: Determining atomic numbers from atomic symbols which are case sensitive.
-- 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.

Running: /home/lanselibai/miniconda3/envs/AmberTools21/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
/bin/bash: /home/lanselibai/miniconda3/envs/AmberTools21/lib/libtinfo.so.6: no version information available (required by /bin/bash)

Running: /home/lanselibai/miniconda3/envs/AmberTools21/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
/bin/bash: /home/lanselibai/miniconda3/envs/AmberTools21/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Info: Total number of electrons: 128; net charge: 0

Running: /home/lanselibai/miniconda3/envs/AmberTools21/bin/mopac.sh
sh: 1: /home/lanselibai/miniconda3/envs/AmberTools21/bin/mopac.sh: not found
/home/lanselibai/miniconda3/envs/AmberTools21/bin/wrapped_progs/antechamber: Fatal Error!
Cannot properly run "/home/lanselibai/miniconda3/envs/AmberTools21/bin/mopac.sh".

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/bin/sh: 1: -i: not found
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'EPE_AC.prmtop'
Total time of execution: less than a second

After looking at the 4th thread, I copy /home/lanselibai/miniconda3/envs/AmberTools21/amber.sh to the last line of /home/lanselibai/.bashrc.
Then I restart the WSL and run acpype -i EPE.mol2, still the mopac problem

Running: /home/lanselibai/miniconda3/envs/AmberTools21/bin/mopac.sh
sh: 1: /home/lanselibai/miniconda3/envs/AmberTools21/bin/mopac.sh: not found
/home/lanselibai/miniconda3/envs/AmberTools21/bin/wrapped_progs/antechamber: Fatal Error!
Cannot properly run "/home/lanselibai/miniconda3/envs/AmberTools21/bin/mopac.sh".
18

Dear Ianselibai,
Did you install acpype via Conda, didn’t you?
Try to uninstall it (I don’t know how to make this, unfortunately) and reinstall via git.
Take a look here: ACPYPE | acpype

I used the git and have acpype installed without any headache!

Paulo A.

19

I was using
pip install acpype

But as Paulo said, I should refer to

, in which it is said " note that pip install acpype , unfortunately, is not picking the original one.". (OMG!!!)

So I unstall the acpype, then

pip install git+https://github.com/alanwilter/acpype.git

Then test it with
acpype -i EPE.pdb
It works!!! The same output as the webserver!!!

Millions of thanks to Paulo A.!

1 Like
20

I’m sorry for all this inconveniences you faced @lanselibai but now ACPYPE has been addressed almost all of this installation issues.

Even if you’re not having issues anymore, have a look at the README here again.

1 Like