Missing ANTECHAMBER library on Windows

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.3rc202110222254 (2021-10-22 22:54:52 UTC)
Description
Missing library(ies?) for ANTECHAMBER in Windows.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3rc202110222254 (2021-10-22)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3io0 format mmcif fromDatabase pdb

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #1  
---  
Chain | Description | UniProt  
A | EtuB protein | A5N734_CLOK5  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> al ATP

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 12 residues in model #1 to IUPAC-IUB
standards.  
3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0  
---  
Chain | Description | UniProt  
1.2/A | EtuB protein | A5N734_CLOK5  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Deleted the following atoms from residue ATP A2: HOA2, HOB2, HOG2, HOG3  
Done loading forcefield  

> hide ~sel

> delete ~sel

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 3io0_A SES surface #1.2.4: minimum, -27.09, mean -9.47,
maximum 1.72  

> al IMD

Fetching CCD IMD from http://ligand-expo.rcsb.org/reports/I/IMD/IMD.cif  
Loading residue template for IMD from internal database  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue IMD (net charge +1) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\tristan\AppData\Local\Temp\tmp_z_qttwn\ante.in.mol2 -fi mol2 -o
C:\Users\tristan\AppData\Local\Temp\tmp_z_qttwn\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n  
(IMD) ``  
(IMD) `Welcome to antechamber 20.0: molecular input file processor.`  
(IMD) ``  
(IMD) `Info: Finished reading file
(C:\Users\tristan\AppData\Local\Temp\tmp_z_qttwn\ante.in.mol2); atoms read
(10), bonds read (10).`  
(IMD) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(IMD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(IMD) `C:/Program Files/ChimeraX/bin/amber20/bin/sh.exe: error while loading
shared libraries: cygreadline7.dll: cannot open shared object file: No such
file or directory`  
(IMD) `/usr/bin/antechamber: Fatal Error!`  
(IMD) `Cannot properly run ""C:/Program
Files/ChimeraX/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0
-o ANTECHAMBER_BOND_TYPE.AC -f ac".`  
Failure running ANTECHAMBER for residue IMD Check reply log for details  




OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
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    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
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    ChimeraX-gltf: 1.0
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    ChimeraX-SaveCommand: 1.5
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    ChimeraX-SDF: 2.0
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    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
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    ChimeraX-WavefrontOBJ: 1.0
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[Eric Pettersen]

Greg, do we have a Windows machine where Cygwin _isn't_ installed? Snow and huck have it installed and james is Windows 7...

[Eric Pettersen]

At any rate, I'm pushing a fix for this, but it would be nice to reproduce it and then verify that the fix remedies it...

[Greg Couch]

We need cygwin for the build process, so AFAIK we don't have any Windows systems without cygwin.

[Eric Pettersen]

I guess Tristan will have to be the guinea pig for this!

[Tristan Croll]

Can try tomorrow. Will it be in the daily build, rc, or both?

[Eric Pettersen]

If all goes well, both.

[Tristan Croll]

Three more libraries needed by sh.exe:

cygintl-8.dll
cygncursesw-10.dll
cygiconv-2.dll

Running the rest of the executables in amber20\bin without arguments doesn't lead to any further linking errors (ncgen and ncgen3 appear to hang - but since I have no idea what they're supposed to do, I don't know if that's normal).
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 17 November 2021 19:12
Cc: gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5619: Missing ANTECHAMBER library on Windows

#5619: Missing ANTECHAMBER library on Windows
----------------------------------------+----------------------------
          Reporter:  Tristan Croll      |      Owner:  Eric Pettersen
              Type:  defect             |     Status:  accepted
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------------

Comment (by Eric Pettersen):

 If all goes well, both.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5619#comment:7>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Okay, added those libs -- hope it works tomorrow!

[Tristan Croll]

Working now! I do still get a warning written to the log after each individual step in the ANTECHAMBER pipeline:

bash.exe: warning: could not find /tmp, please create!

... but it doesn't actually seem to be causing any problem.

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 18 November 2021 22:00
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5619: Missing ANTECHAMBER library on Windows

#5619: Missing ANTECHAMBER library on Windows
----------------------------------------+----------------------------
          Reporter:  Tristan Croll      |      Owner:  Eric Pettersen
              Type:  defect             |     Status:  accepted
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * cc: Tom Goddard (added)


Comment:

 Okay, added those libs -- hope it works tomorrow!

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5619#comment:9>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Yeah, I have tried a variety of things to get rid of that /tmp "warning", to no avail. Just going to live with it for now.

[Tristan Croll]

In build 1.3rc202112010754 those last three libraries (cygintl-8.dll, cygncursesw-10.dll and cygiconv-2.dll) are missing again. In the amber20/bin directory I see:

22/08/2021 01:30 75,283 cyggcc_s-seh-1.dll
20/01/2018 00:24 1,202,195 cyggfortran-3.dll
08/12/2018 17:02 1,785,875 cyggfortran-4.dll
22/08/2021 01:30 2,871,827 cyggfortran-5.dll
22/08/2021 01:30 363,027 cygquadmath-0.dll
30/08/2021 22:55 259,603 cygreadline7.dll
08/11/2021 08:57 3,549,431 cygwin1.dll

[Eric Pettersen]

Someone who shall remain nameless compiled from out of date source on a Windows box, which wound up uploading an AmberTools archive missing those files.

I have replaced that archive with one containing the missing libraries and will be testing the build tomorrow on a Windows machine we just got that does not have Cygwin installed (already verified that the current release candidate fails on that machine as per your description).

[Tristan Croll]

Received a message from Daniel Asarnow this morning:

I noticed that in order for antechamber to run on Windows, a directory named tmp must be created in ChimeraX/bin/amber20. After that ISOLDE's ligand parameterization macro works just fine on Windows.

If it's *actually* failing for him without it I'm surprised (works fine on my Windows machine), but I just tried and creating the tmp directory there does indeed suppress that annoying bash warning.

[Eric Pettersen]

I have added that tmp directory starting with tomorrow's build.