Hello,
Following on from my previous message (
http://archive.ambermd.org/202305/0137.html), I have managed to move forward - it seems that amber16 has a problem recognising OW, whereas in amber09 it is fine. However, by running the next step: `MCPB.py -i PTT.in -s 2` an error appears (below). What could be the cause of this? Here is the link to my cloud where I uploaded all the files —
https://student.cloud.umw.edu.pl/index.php/s/gqWHmtB3Bpe9nCN <
https://student.cloud.umw.edu.pl/index.php/s/gqWHmtB3Bpe9nCN> .
Thank you in advance,
Maciej
******************************************************************
* Welcome to use the MCPB.py program *
* Version 2.0 *
* Author: Pengfei Li *
* Merz Research Group *
* Michigan State University *
******************************************************************
The input file you are using is : PTT.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is : [33, 34]
The variable ion_info is : []
The variable ion_mol2files is : ['PT.mol2']
The variable original_pdb is : PTT.pdb
The variable add_bonded_pairs is : []
The variable additional_resids is : []
The variable anglefc_avg is : 0
The variable bondfc_avg is : 0
The variable cut_off is : 2.8
The variable chgfix_resids is : []
The variable force_field is : ff14SB
The variable frcmodfs is : ['ISO.frcmod']
The variable gaff is : 1
The variable group_name is : PTT
The variable ion_paraset is : CM (Only for nonbonded model)
The variable large_opt is : 0
The variable lgmodel_chg is : -99
-99 means program will assign a charge automatically.
The variable naa_mol2files is : ['ISO.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
-99 means program will assign a charge automatically.
The variable software_version is : g03
The variable sqm_opt is : 0
The variable water_model is : TIP3P
******************************************************************
* *
*===================Generate the Initial frcmod file=============*
* *
******************************************************************
Atoms which has changed the atom types: [5, 17, 33, 34, 35]
1-ISO.5-N : nd --> Y1
2-ISO.17-N : nd --> Y2
3-PT.33-PT : PT --> M1
4-CL.34-CL : CL --> Y3
5-WAT.35-O : OW --> Y4
==================Using the Seminario method to solve the problem.
=======================Generate the bond parameters===============
For bondtype: M1-Y3. There are 1 bond(s) in this type:
The bond length(s) is(are): [2.2916]
The average bond length is: 2.2916 Angstrom.
The force constant(s) is(are): [155.0]
The average force constant is: 155.0 Kcal*mol^-1*A^-2.
For bondtype: M1-Y4. There are 1 bond(s) in this type:
The bond length(s) is(are): [2.1798]
The average bond length is: 2.1798 Angstrom.
The force constant(s) is(are): [73.0]
The average force constant is: 73.0 Kcal*mol^-1*A^-2.
For bondtype: Y1-M1. There are 1 bond(s) in this type:
The bond length(s) is(are): [2.0353]
The average bond length is: 2.0353 Angstrom.
The force constant(s) is(are): [123.7]
The average force constant is: 123.7 Kcal*mol^-1*A^-2.
For bondtype: Y2-M1. There are 1 bond(s) in this type:
The bond length(s) is(are): [2.0285]
The average bond length is: 2.0285 Angstrom.
The force constant(s) is(are): [128.6]
The average force constant is: 128.6 Kcal*mol^-1*A^-2.
/opt/exp_soft/local/skylake/amber/16/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py:329: RuntimeWarning: invalid value encountered in double_scalars
vec12 = [i/(disbohr) for i in vec12]
For bondtype: Y3-Y3. There are 1 bond(s) in this type:
The bond length(s) is(are): [0.0]
The average bond length is: 0.0 Angstrom.
The force constant(s) is(are): [nan]
The average force constant is: nan Kcal*mol^-1*A^-2.
=======================Generate the angle parameters==============
For angletype: M1-Y2-cc. There are 1 angle(s) in this type:
The angle value(s) is(are): [135.66]
The average angle value is: 135.66 Degree.
The force constant(s) is(are): [156.35]
The average force constant is: 156.35 Kcal*mol^-1*Rad^-2.
/opt/exp_soft/local/skylake/amber/16/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py:126: ComplexWarning: Casting complex values to real discards the imaginary part
afconst = [round(i, 2) for i in afconst]
For angletype: M1-Y2-os. There are 1 angle(s) in this type:
The angle value(s) is(are): [115.27]
The average angle value is: 115.27 Degree.
The force constant(s) is(are): [167.81]
The average force constant is: 167.81 Kcal*mol^-1*Rad^-2.
/opt/exp_soft/local/skylake/amber/16/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py:399: RuntimeWarning: invalid value encountered in double_scalars
vec32 = array([i/dis32 for i in vec32])
Traceback (most recent call last):
File "/opt/exp_soft/local/skylake/amber/16/bin/MCPB.py", line 580, in <module>
fcfchkf, fclogf, g0x, scalef, bondfc_avg, anglefc_avg)
File "/opt/exp_soft/local/skylake/amber/16/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py", line 719, in gene_by_QM_fitting_sem
angval, fcfinal = get_ang_fc_with_sem(crds, fcmatrix, nat1, nat2, nat3, scalef, angavg)
File "/opt/exp_soft/local/skylake/amber/16/lib/python2.7/site-packages/mcpb/gene_final_frcmod_file.py", line 401, in get_ang_fc_with_sem
angval = calc_angle(crd1, crd2, crd3)
File "/opt/exp_soft/local/skylake/amber/16/lib/python2.7/site-packages/msmtmol/cal.py", line 18, in calc_angle
tempval = (d23**2+d12**2-d13**2)/(2*d12*d23)
ZeroDivisionError: float division by zero
--
Maciej Spiegel, MPharm
Department of Pharmacognosy and Herbal Medicines
Wroclaw Medical University
https://farmaceut.github.io <https://farmaceut.github.io/>
.ORCiD <https://orcid.org/0000-0002-8012-1026> @Publons <https://publons.com/researcher/4419515/maciej-spiegel/>
Reviewer at:
Phytochemistry | Free Radical Research | Theoretical Chemistry Accounts
Journal of Molecular Modeling | Frontiers in Bioscience-Landmark | Symmetry
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Received on Sun Jun 04 2023 - 04:00:02 PDT
