Mohammed Nooraldeen Al-Qattan

University of Science Malaysia | USM · Centre for Drugs Research (CDR)

Alsallam alaykom. I am using rdkit and py3dmol in pycharm, where I faced problem in making drawings visible.

it gives me for rdkit drawings:

<IPython.core.display.Image object>

and for py3dmol drawings gives nothing.

In jupyter everthing is going OK

the full code is provided below

import py3Dmol import copy from rdkit import Chem from rdkit.Chem import Draw from rdkit.Chem.Draw import IPythonConsole from rdkit.Chem import AllChem from rdkit.Chem import rdBase from rdkit.Chem import rdMolAlign from rdkit.Chem import rdMolDescriptors import numpy as np import streamlit as st p=AllChem.ETKDGv3() p.verbose=True mols=[m for m in Chem.SDMolSupplier('cdk2.sdf') if m !=None] [:2] for mol in mols: mol.RemoveAllConformers() hmols_1=[Chem.AddHs(m) for m in mols] hmols_2=copy.deepcopy(hmols_1) #generate 100 conformers per molcule for mol in hmols_1: AllChem.EmbedMultipleConfs(mol,100,p) for mol in hmols_2: AllChem.EmbedMultipleConfs(mol,100,p) writer=Chem.SDWriter('hmols_1.sdf') for mol in hmols_1: writer.write(mol) #import matplotlib.pyplot as plt #import PIL as pl #Draw.MolsToGridImage(mols) #fig.show() #from IPython.display import display, Image Draw.MolsToGridImage(mols) #IPythonConsole.display.display(fig) #fig.show() #.MolsToGridImage(mols) #st.image(Draw._drawerToImage().show()) # %% ### assignign force field scores crippen_contribs=[rdMolDescriptors._CalcCrippenContribs(mol) for mol in hmols_1] crippen_ref_contrib=crippen_contribs[0] crippen_prob_contribs=crippen_contribs[1:] ref_mol1=hmols_1[0] prob_mols_1=hmols_1[1:] mmff_params=[AllChem.MMFFGetMoleculeProperties(mol) for mol in hmols_2] mmff_ref_param=mmff_params[0] mmff_prob_params=mmff_params[1:] ref_mol2=hmols_2[0] prob_mols_2=hmols_2[1:] # %% ## allign using forcefield p_crippen=py3Dmol.view(width=600, height=400) p_crippen.addModel(Chem.MolToMolBlock(ref_mol1),'sdf') crippen_score=[] for idx, mol in enumerate(prob_mols_1): tempscore=[] for cid in range (100): crippenO3A=rdMolAlign.GetCrippenO3A(mol,ref_mol1,crippen_prob_contribs[idx],crippen_ref_contrib,cid,0) crippenO3A.Align() tempscore.append(crippenO3A.Score()) best=np.argmax(tempscore) p_crippen.addModel (Chem.MolToMolBlock(mol,confId=int(best)),'sdf') crippen_score.append(tempscore[best]) #p_crippen.setStyle({'stick': {}}) p_crippen.render() p_crippen p_crippen.show()

How to do conformational search before DFT calculations in Gaussian WITHOUT using gmmx add-on.

I have tried using spartan and pcmodel but the conformation obtained cannot be used directly in DFT calculation; it gives error "no special actions if energy rises".

therefore, I tried using PM6 and AM1 semi-emiprical calculations before doing DFT but also gave errors "restarting incremental Fock formation" and "AX will form 1A0 Fock derivatives at one time"

I have problem with simulating pr-lig complex where ligand has halogens like Cl or Br.

by preparing itp files using CgenFF server or Charmm-gui , i get an atom type LP1 and LP2 connected to the halgen. which makes me suspicious about the result.

Should I keep or remove those strange atoms (LP1 and LP2) ?

should I use another way to prepare the itp files ?

I have 144 diffraction images for a crystal of high mosaicity about 2 and low resolution about 3.14.

the crystal has been prepared and soaked with ligand. I would like to solve the crystal structure looking merely for a substrate binding site.

I tried using IMosflm, however the results of integration showed that all reflections are partial and there is no full reflection at all.

Then I used scala from CCP4 to do 2D integration for partial reflections, then check the density map using molecular replacement (protein has been deposited in PDB) with Phoenix. I can Max have LLG 900 and TFZ of 11. I can only recognize coarse features like helices, however the map is not clear for many side chains as well as at the binding site.

Any suggestion to improve the results using parameters adjustment of iMosflm, Scala, Phoenix MR. OR even new suggested software.

I appreciate any suggestion.

thanks

Although it is familiar in molecular biology, I could not found it in literature.

Using QM/MM is known to stimulate bond formation and breaking, however, how to drag this reaction to take place in AMBER.

If I am to use the simplified bond formation and breaking force field (Reaxff), how to incorporate it into Amber?