Hi Maciej,
I am afraid that this "discarding imaginary" message is a bad sign. This likely means the Gaussian analysis from step 1 generates imaginary frequencies. This means that either the small or the large model is not being calculated correctly by the QM package.
There are several walk-around, and one of them, according to Q2.2 of the MCPB.py FAQ page<
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpyfaq.php>, is to use Z-matrix or empirical methods to generate force constants. To use them, simply call MCPB.py -i <your input file> -s 2z (for Z-matrix method) or MCPB.py -i <your input file> -s 2e (for empirical method).
If it is still failing, a revisit of the Gaussian calculation may be needed.
Best regards,
Zhen.
_____________________
Zhen Li<
http://lizhen62017.wixsite.com/home>, Ph.D.,
The Merz Research Group<
http://merzgroup.org>,
Michigan State University,
Cleveland Clinic.
________________________________
From: maciej.spiegel via AMBER <amber.ambermd.org>
Sent: Friday, August 1, 2025 2:13 PM
To: Jeffrey Wagner <jwagnerjpl.gmail.com>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] MCPB.py Error at Step 2: TypeError with numpy.complex128 in angle parameter generation
Hi Jeff,
Thanks, I got it working — unless the following message is a bad omen:
"/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/lib/python3.13/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py:166:
ComplexWarning: Casting complex values to real discards the imaginary
part print('%8s %7.2f %7.2f %-s' %(angtyp,param[0], param[1],
note), file=finfrcmod)"
Moreover, tleap step fails now with several issues:
"""
/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/teLeap:
Error!
Could not find bond parameter for atom types: Y4 - HO
for atom O at position -1.116000, 0.112000, -3.037000
and atom H1 at position -1.336000, -0.804000, -3.283000.
/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/teLeap:
Error!
Could not find bond parameter for atom types: HO - Y4
for atom H at position -2.016000, 0.519000, -2.641000
and atom O at position -1.116000, 0.112000, -3.037000.
Building angle parameters.
/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/teLeap:
Error!
Could not find angle parameter for atom types: HO - Y4 - HO
for atom H at position -2.016000, 0.519000, -2.641000,
atom O at position -1.116000, 0.112000, -3.037000,
and atom H1 at position -1.336000, -0.804000, -3.283000.
Building proper torsion parameters.
Building improper torsion parameters.
total 8 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/teLeap:
Warning!
Parameter file was not saved.
Solute vdw bounding box: 13.217 8.896 10.247
Total bounding box for atom centers: 33.217 28.896 30.247
Solvent unit box: 18.865 18.478 19.006
Total vdw box size: 36.472 32.030 33.355 angstroms.
Volume: 38965.483 A^3
Total mass 15504.078 amu, Density 0.661 g/cc
Added 831 residues.
/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/teLeap:
Warning!
addIons: 1st Ion & target unit have charges of the same sign:
unit charge = 0.999998; ion1 charge = 1;
can't neutralize.
1 Cl- ion required to neutralize.
Adding 1 counter ions to "mol" using 1A grid
Grid extends from solute vdw + 2.36 to 8.31
Resolution: 1.00 Angstrom.
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
(Replacing solvent molecule)
Placed Cl- in mol at (-4.14, 2.14, -4.40).
Done adding ions.
Writing pdb file: CIX_solv.pdb
printing CRYST1 record to PDB file with box info
Checking Unit.
/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/teLeap:
Note.
Ignoring the warnings from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/teLeap:
Error!
Could not find bond parameter for atom types: Y4 - HO
for atom O at position -1.144589, -0.137137, -3.112954
and atom H1 at position -1.364589, -1.053137, -3.358954.
/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/teLeap:
Error!
Could not find bond parameter for atom types: HO - Y4
for atom H at position -2.044589, 0.269863, -2.716954
and atom O at position -1.144589, -0.137137, -3.112954.
Building angle parameters.
/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/teLeap:
Error!
Could not find angle parameter for atom types: HO - Y4 - HO
for atom H at position -2.044589, 0.269863, -2.716954,
atom O at position -1.144589, -0.137137, -3.112954,
and atom H1 at position -1.364589, -1.053137, -3.358954.
Building proper torsion parameters.
Building improper torsion parameters.
total 8 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/teLeap:
Warning!
Parameter file was not saved.
Quit
"""
W dniu 2025-08-01 18:18, Jeffrey Wagner napisał(a):
> Hi Maciej,
>
> I've never used MCPB but we're seeing some issues in ParmEd arising
> from last month's numpy 2.3 release. Downgrading to a 2.2.X version is
> helping people get around some of those errors and may also help here.
>
> https://urldefense.com/v3/__https://github.com/ParmEd/ParmEd/issues/1406__;!!HXCxUKc!3EmOwMQTNcBv6X6yX-Z13ud6T7ex8pb-68_akEQGUMHknLeEU2YPhK6cXJLHQRLm3Q-zELe-xfShoBMFP4c8MZs$
>
> Cheers,
> Jeff
>
> On Fri, Aug 1, 2025 at 8:24 AM maciej.spiegel via AMBER
> <amber.ambermd.org> wrote:
>
>> Hello Everyone,
>>
>> I am following the MCPB.py tutorial and encountered an error at the
>> step:
>> "MCPB.py -i MCPB.in -s 2"
>>
>> The program starts as expected and parses the input successfully,
>> but
>> then fails during the angle parameter generation using the Seminario
>>
>> method, with the following error:
>>
>> """
>> ******************************************************************
>> * Welcome to use the MCPB.py program *
>> * Version 2024 *
>> * Author: Pengfei Li *
>> * Merz Research Group *
>> * Michigan State University *
>> * AND *
>> * Hammes-Schiffer Research Group *
>> * Yale University *
>> * AND *
>> * Li Research Group *
>> * Loyola University Chicago *
>> ******************************************************************
>> The input file you are using is : MCPB.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>> The following is the input variable you have:
>> The variable ion_ids is : [1]
>> The variable ion_info is : []
>> The variable ion_mol2files is : ['PT.mol2']
>> The variable original_pdb is : CIX.pdb
>> The variable add_bonded_pairs is : []
>> The variable add_redcrd is : 0
>> The variable additional_resids is : []
>> The variable anglefc_avg is : 0
>> The variable bondfc_avg is : 0
>> The variable chgfix_resids is : []
>> The variable cut_off is : 2.8
>> The variable force_field is : ff19SB
>> The variable frcmod_files is : ['ISX.frcmod']
>> The variable gaff is : 1
>> The variable group_name is : CIX
>> The variable ion_paraset is : 12_6 (Only for the ions using the
>> nonbonded model).
>> The variable large_opt is : 1
>> The variable lgmodel_chg is : -99
>> The variable lgmodel_spin is : -99
>> -99 means program will assign a charge automatically.
>> The variable naa_mol2files is : ['ISX.mol2', 'WAT.mol2', 'CL.mol2']
>> The variable scale_factor is : 1.0
>> ATTENTION: This is the scale factor of frequency. The
>> force constants will be scaled by multiplying the
>> square
>> of scale_factor.
>> The variable smmodel_chg is : -99
>> The variable smmodel_spin is : -99
>> -99 means program will assign a charge automatically.
>> The variable software_version is : gau
>> The variable sqm_opt is : 0
>> The variable water_model is : OPC
>> The variable xstru is : 0
>> ******************************************************************
>> * *
>> *===================Generate the Initial frcmod file=============*
>> * *
>> ******************************************************************
>> Atoms which has changed the atom types: [1, 2, 18, 34, 36]
>> 1-PT.1-PT : PT --> M1
>> 2-ISX.2-N1 : n2 --> Y1
>> 3-ISX.18-N1 : n2 --> Y2
>> 4-CL.34-CL : Cl --> Y3
>> 5-WAT.36-O : OW --> Y4
>> ******************************************************************
>> * *
>> *=========Using the Seminario method to solve the problem========*
>> * *
>> ******************************************************************
>> =======================Generate the bond parameters===============
>> For bondtype: M1-Y1. There are 1 bond(s) in this type:
>> The bond length(s) is(are): [2.0637]
>> The average bond length is: 2.0637 Angstrom.
>> The force constant(s) is(are): [np.float64(103.8)]
>> The average force constant is: 103.8 Kcal*mol^-1*A^-2.
>> For bondtype: M1-Y2. There are 1 bond(s) in this type:
>> The bond length(s) is(are): [1.9964]
>> The average bond length is: 1.9964 Angstrom.
>> The force constant(s) is(are): [np.float64(144.8)]
>> The average force constant is: 144.8 Kcal*mol^-1*A^-2.
>> For bondtype: M1-Y3. There are 1 bond(s) in this type:
>> The bond length(s) is(are): [2.311]
>> The average bond length is: 2.311 Angstrom.
>> The force constant(s) is(are): [np.float64(140.6)]
>> The average force constant is: 140.6 Kcal*mol^-1*A^-2.
>> For bondtype: M1-Y4. There are 1 bond(s) in this type:
>> The bond length(s) is(are): [2.1182]
>> The average bond length is: 2.1182 Angstrom.
>> The force constant(s) is(are): [np.float64(87.7)]
>> The average force constant is: 87.7 Kcal*mol^-1*A^-2.
>> =======================Generate the angle parameters==============
>> For angletype: M1-Y1-c1. There are 1 angle(s) in this type:
>> The angle value(s) is(are): [134.7]
>> The average angle value is: 134.7 Degree.
>> The force constant(s) is(are): [np.float64(143.92)]
>> The average force constant is: 143.92 Kcal*mol^-1*Rad^-2.
>> Traceback (most recent call last):
>> File
>>
> "/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/bin/MCPB.py",
>>
>> line 682, in <module>
>> gene_by_QM_fitting_sem(smpdbf, ionids, xstru, stfpf, prefcdf,
>> finfcdf,
>>
>>
> ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>> fcfchkf, fclogf, g0x, scalef, bondfc_avg, anglefc_avg)
>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>> File
>>
> "/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/lib/python3.13/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py",
>>
>> line 835, in gene_by_QM_fitting_sem
>> ang_para = avg_angle_para(misangat123, angvals, afconst)
>> File
>>
> "/mnt/storage_2/project_data/pl0251-02/bin/miniconda3/envs/AmberTools24/lib/python3.13/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py",
>>
>> line 131, in avg_angle_para
>> afconst = [round(i, 2) for i in afconst]
>> ~~~~~^^^^^^
>> TypeError: type numpy.complex128 doesn't define __round__ method
>> """
>>
>> It seems that the program is attempting to round a value of type
>> numpy.complex128, which leads to a TypeError since complex numbers
>> cannot be directly rounded.
>>
>> For convenience, I’ve made all the relevant input files available
>> in
>> this GitHub repository:
>> https://urldefense.com/v3/__https://github.com/farmaceut/ERROR_MCPB.py.git__;!!HXCxUKc!3EmOwMQTNcBv6X6yX-Z13ud6T7ex8pb-68_akEQGUMHknLeEU2YPhK6cXJLHQRLm3Q-zELe-xfShoBMFYyJu8ow$
>>
>> Has anyone encountered a similar issue? Any suggestions or insights
>> on
>> how to resolve this would be greatly appreciated.
>> Thank you in advance !
>> -
>> Maciej Spiegel, MPharm PhD
>> assistant professor
>>
>> Department of Organic Chemistry and Pharmaceutical Technology,
>> Faculty of Pharmacy, Wroclaw Medical University
>> Borowska 211A, 50-556 Wroclaw, Poland
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!HXCxUKc!3EmOwMQTNcBv6X6yX-Z13ud6T7ex8pb-68_akEQGUMHknLeEU2YPhK6cXJLHQRLm3Q-zELe-xfShoBMFw0R7Ya4$
--
-
Maciej Spiegel, MPharm PhD
assistant professor
Department of Organic Chemistry and Pharmaceutical Technology,
Faculty of Pharmacy, Wroclaw Medical University
Borowska 211A, 50-556 Wroclaw, Poland
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Received on Fri Aug 01 2025 - 11:30:03 PDT
