sqm suggestions

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3rc202112010754 (2021-12-01 07:54:47 UTC)
Description
Trying to parameterise the residue TPP (attached) fails with a rather unhelpfully vague "Fatal Error" in sqm. After some digging around I finally worked out that the actual error is only reported at the end of the sqm.out file. In this case:

QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after   1000 steps.
QMMM: E =  -0.7947E+06 DeltaE =  -0.5632E+02 DeltaP =   0.5919E+00
QMMM: Smallest DeltaE =  -0.1532E+01 DeltaP =   0.6645E+00 Step =     42

Would probably be a good idea to pull that out and report it in cases like this.

I also noticed that if antechamber is run without the explicit "-ek qm_theory='AM1'," some extra parameters get written to the sqm.in file:

With the explicit -ek switch:

Run semi-empirical minimization
 &qmmm
  qm_theory=AM1,  qmcharge=-2,

Without:

Run semi-empirical minimization
 &qmmm
    qm_theory='AM1', grms_tol=0.0005,
 scfconv=1.d-10, ndiis_attempts=700,   qmcharge=-2,

With that second set of parameters it succeeds approximately 2 out of 3 times (takes a few minutes, though) - probably mostly down to the ndiis_attempts argument (according to the manual the default is zero, and it recommends setting it to a high value - maximum 1000 - for difficult cases). Might be worth making this the default?


Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> 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: 1.3rc202112010754 (2021-12-01)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /run/media/tic20/storage/structure_dump/aus/yu_shang/TPP_ideal.pdb
> format pdb

> select /A:1@HOA2

1 atom, 1 residue, 1 model selected  

> select add /A:1@HOB2

2 atoms, 1 residue, 1 model selected  

> select add /A:1@HOB3

3 atoms, 1 residue, 1 model selected  

> delete sel

> select /A:1@C7

1 atom, 1 residue, 1 model selected  

> select up

42 atoms, 43 bonds, 1 residue, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue TPP (net charge -2) with am1-bcc method  
Running ANTECHAMBER command: /usr/libexec/UCSF-
ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpmylky6ut/ante.in.mol2 -fi mol2 -o /tmp/tmpmylky6ut/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(TPP) ``  
(TPP) `Welcome to antechamber 20.0: molecular input file processor.`  
(TPP) ``  
(TPP) `Info: Finished reading file (/tmp/tmpmylky6ut/ante.in.mol2); atoms read
(42), bonds read (43).`  
(TPP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(TPP) `Running: /usr/libexec/UCSF-ChimeraX/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(TPP) ``  
(TPP) ``  
(TPP) `Running: /usr/libexec/UCSF-ChimeraX/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(TPP) `Info: Total number of electrons: 220; net charge: -2`  
(TPP) ``  
(TPP) `Running: /usr/libexec/UCSF-ChimeraX/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(TPP) `/usr/libexec/UCSF-ChimeraX/bin/amber20/bin/antechamber: Fatal Error!`  
(TPP) `Cannot properly run "/usr/libexec/UCSF-ChimeraX/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue TPP Check reply log for details  

> ui mousemode right "bond rotation"

> torsion /A:1@C4',C5',C7',N3 166.75

> torsion /A:1@C4',C5',C7',N3 53.75

> torsion /A:1@C4',C5',C7',N3 145.75

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue TPP (net charge -2) with am1-bcc method  
Running ANTECHAMBER command: /usr/libexec/UCSF-
ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpk8mi3ls7/ante.in.mol2 -fi mol2 -o /tmp/tmpk8mi3ls7/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(TPP) ``  
(TPP) `Welcome to antechamber 20.0: molecular input file processor.`  
(TPP) ``  
(TPP) `Info: Finished reading file (/tmp/tmpk8mi3ls7/ante.in.mol2); atoms read
(42), bonds read (43).`  
(TPP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(TPP) `Running: /usr/libexec/UCSF-ChimeraX/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(TPP) ``  
(TPP) ``  
(TPP) `Running: /usr/libexec/UCSF-ChimeraX/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(TPP) `Info: Total number of electrons: 220; net charge: -2`  
(TPP) ``  
(TPP) `Running: /usr/libexec/UCSF-ChimeraX/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(TPP) `/usr/libexec/UCSF-ChimeraX/bin/amber20/bin/antechamber: Fatal Error!`  
(TPP) `Cannot properly run "/usr/libexec/UCSF-ChimeraX/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue TPP Check reply log for details  

> torsion /A:1@C4',C5',C7',N3 -167.25

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue TPP (net charge -2) with am1-bcc method  
Running ANTECHAMBER command: /usr/libexec/UCSF-
ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpc8yb65in/ante.in.mol2 -fi mol2 -o /tmp/tmpc8yb65in/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(TPP) ``  
(TPP) `Welcome to antechamber 20.0: molecular input file processor.`  
(TPP) ``  
(TPP) `Info: Finished reading file (/tmp/tmpc8yb65in/ante.in.mol2); atoms read
(42), bonds read (43).`  
(TPP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(TPP) `Running: /usr/libexec/UCSF-ChimeraX/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(TPP) ``  
(TPP) ``  
(TPP) `Running: /usr/libexec/UCSF-ChimeraX/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(TPP) `Info: Total number of electrons: 220; net charge: -2`  
(TPP) ``  
(TPP) `Running: /usr/libexec/UCSF-ChimeraX/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(TPP) `/usr/libexec/UCSF-ChimeraX/bin/amber20/bin/antechamber: Fatal Error!`  
(TPP) `Cannot properly run "/usr/libexec/UCSF-ChimeraX/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue TPP Check reply log for details  




OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G          9G         32G        299M         19G         51G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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File attachment: TPP.mol2

TPP.mol2​

[Tristan Croll]

Added by email2trac

[Tristan Croll]

One other minor thing: the antechamber command reported to the log:

ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmpmylky6ut/ante.in.mol2 -fi mol2 -o /tmp/tmpmylky6ut/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n

... doesn't work when copied to the shell (with in and out filenames replaced accordingly, of course). The error message is a bit confusing (sqm complains that it can't find the method am1 in its lookup table), but ultimately it's just that the bit after -ek needs to be quoted:

ChimeraX/bin/amber20/bin/antechamber -ek "qm_theory='AM1'," -i /tmp/tmpmylky6ut/ante.in.mol2 -fi mol2 -o /tmp/tmpmylky6ut/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n

[Eric Pettersen]

The reporting of sqm output has already been done separately.

Though it looks like omitting the '-ek...' flag does more reliably produce a set of charges but it's not all upside -- it seems to be significantly slower than providing the flag, namely 47% slower (average of 30.4 seconds slower) across 10 quasi-random compounds (data below). So I think the plan here is to try the faster method first and if that produces a convergence failure then try again with the slower method.

Timings (in seconds) done with FMN from 3fx2 and 9 PubChem IDs:

compound: no flag → with flag

FMN: 104 → 70
54670067: 8 → 20
143: 194 → 91
1428: 190 → 180
49274: 31 → 29
423567: 80 → 40
481667: 68 → 103
135399: 109 → 38
11907: 2 → 2
7071025: 170 → 79

total: 956 → 652

[Eric Pettersen]

Charge computation falls back to no -ek flag if using the flag result in convergence failure: ​https://github.com/RBVI/ChimeraX/commit/0ace3fbbedf48a60c40cee6a6569789ab21ca0de