Open ZeroDesigner opened 3 years ago
Your BNZ
residue doesn't have any hydrogens!
HETATM 2636 C1 BNZ A 200 -32.969 6.196 2.877 1.00 0.00 C
HETATM 2637 C2 BNZ A 200 -32.945 7.046 3.973 1.00 0.00 C
HETATM 2638 C3 BNZ A 200 -33.719 6.798 5.113 1.00 0.00 C
HETATM 2639 C4 BNZ A 200 -34.540 5.680 5.143 1.00 0.00 C
HETATM 2640 C5 BNZ A 200 -34.545 4.825 4.044 1.00 0.00 C
HETATM 2641 C6 BNZ A 200 -33.787 5.069 2.915 1.00 0.00 C
openmmforcefields
is only able to apply parameters to atoms that are there. You'll need to regenerate your PDB file in a manner that all of the atoms in any small molecules you want to parameterize are already there as HETATM
cards with corresponding CONECT
records.
@Jiaqi-Su Did this fix your issue?
@Jiaqi-Su Did this fix your issue?
Sorry so late to reply. With your opinion, I have fixed it. The process is that : 1 PyMol is used to add hydrogen; 2:fixed the complex; 3:run the code of example . And I am trying to make it easier. I am trying to write a script to automate the processing of complex structure. I will make a comment after I finish the script.
Great!
You can use Python toolkits like the RDKit or the OpenEye Toolkit to automate this if you want a complete Python solution!
Great!
You can use Python toolkits like the RDKit or the OpenEye Toolkit to automate this if you want a complete Python solution!
Yes, they just are the toolkits what I am using now.
@Jiaqi-Su Did this fix your issue?
Sorry so late to reply. With your opinion, I have fixed it. The process is that : 1 PyMol is used to add hydrogen; 2:fixed the complex; 3:run the code of example . And I am trying to make it easier. I am trying to write a script to automate the processing of complex structure. I will make a comment after I finish the script.
hello, i had the same problem, so i want to know how you fixed the complex?
Hi I try to reproduce the example you offered. the code is below.
and the error is:
How can I finish it?
the 4w52_ben_fixed_h.pdb