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Quickstart example fails #565
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Hi, sorry again about the outdated info, we are working on overhauling the docs and supply more up to date examples To load up the OPLSAA force field:
Regarding the ethane example, that file used to work before, but there might have been changes our dependency's reader that causing the error. You can try to create the compound the smiles string (with mbuild) instead to test that out
For the styrene molecule, it appears that the current oplsaa force field XML is missing two dihedral parameters (I am guessing the part C=C sticking out from the aromatic ring). You can either find the parameters from the literature and add those in the XML file (
|
Hello again @daico007 and thanks for your reply! I'm looking forward for you to update the Foyer docs, since it's not entirely clear how to work with it except for digging into the source code. For instance, if you didn't provide me with instructions, I would not know how to apply OPLS-AA in Foyer correctly. I've tried what you suggested and got some more warnings [ working with your latest Foyer container with Python 3.9.19 ] . To be precise, since I don't have a superuser rights on the Linux-driven machine that I'm working with, I create a Given your fixes, I believe that Quickstart example should now be looking like :
Does it look correct?
Is it also OK? Nonetheless, both Once, I also got some error related to
Does it make any difference, which one to call inside the container :
Given your comment, I build the following work-around example:
which led to the following warnings :
Nonetheless, it seemed to work, i.e. Regarding editing |
Hi again, @daico007 ! I got a general Q. Do I understand it correctly that if one applies OPLS-AA forcefield to some complicated molecule and the error is :
then, it means that there is no corresponding info in I got the same error message for both
next command was either :
or
then, FF :
and it's application either via :
or :
As a result, I always got the error like written above. The molecule isn't that large and complicated, it's 6PPD basically, i.e. C18--H24--N2. |
Hi @iGulitch, sorry for the slow responses, @daico007 was actually defending his Ph.D. thesis around then, so I'm guessing that's why he didn't get back to you. I was passing back through some messages and realized you never got a response here. So here's what I got.
You can check what that molecule is by looking at the fourth index of the compound. for i, part in enumerate(mol.particles()): # tell you what particle is missing
if i == 4:
break
print(f"Missing atom is {part}")
for bond in mol.bonds(): # tell you what bonds the missing atom has
if part in bond: # bond is a tuple of the two particles that make it up
print(f"{bond=}) |
Hi, @CalCraven ! Many thanks for the suggestion! I'll give a try. Best regards, @iGulitch P.S. I hope @daico007 made it successfully with his Ph.D. thesis defense :) |
Quickstart example fails / is wrong / outdated :
mol = parmed.load("ethane.pdb")
- notload
, butload_file
Moreover, when using provided
ethane.pdb
molecule from./docs/source/files/
, got the error:I tried benzene ring and styrene molecule instead, and it worked.
ff = foyer.forcefield.load_OPLSAA()
- noload_OPLSAA
attiribute in modulefoyer.forcefield
, but there is one infoyer.forcefields
. Trying out the latter ...worked for benzene. However, for styrene, the line
mol_ff = ff.apply(mol)
gave :Thus, no further save of
*.gro
and*.top
files is possible.Please, help to understand how to make Foyer working.
P.S. I followed the official Installation workflow via
git
, viaconda install
and even tried out your Docker container. The results are the same.The text was updated successfully, but these errors were encountered: