Gromacs Wizard Protein-Ligand MD preparation error
-
Hello everyone,
I am trying to run a MD simulation of my protein-ligand complex. Given the situation with the incorrectly parametrized Gromos forcefields, I've been trying to run the simulation using Chramm36. I parametrized my ligand using the CGenFF website, and downloaded the Gromacs-converted files. These files include the following:
a copy of the charmm36.ff, with the files LIG.rtp and LIG_ffbonded.itp files within the forcefield directory;
LIG.pdb;
and LIG.top.When trying to prepare the system, I get the following error from the Gromacs Wizard:
Fatal error:There were 19 missing atoms in molecule Other_chain_B, if you want to use thisincomplete topology anyhow, use the option -missingWith the actual Gromacs Error being:
Making bonds...
atom H26 is missing in residue GK2 1 in the pdb file
You might need to add atom H26 to the hydrogen database of building block GK2 in the file GK2.hdb (see the manual)
atom H27 is missing in residue GK2 1 in the pdb file...I understand this is an issue of a missing file from CGenFF, given that there is no GK2.hdb provided in the charmm36.ff directory, but how should I go about solving this?
Thanks for your help.
-
Hello everyone,
I am trying to run a MD simulation of my protein-ligand complex. Given the situation with the incorrectly parametrized Gromos forcefields, I've been trying to run the simulation using Chramm36. I parametrized my ligand using the CGenFF website, and downloaded the Gromacs-converted files. These files include the following:
a copy of the charmm36.ff, with the files LIG.rtp and LIG_ffbonded.itp files within the forcefield directory;
LIG.pdb;
and LIG.top.When trying to prepare the system, I get the following error from the Gromacs Wizard:
Fatal error:There were 19 missing atoms in molecule Other_chain_B, if you want to use thisincomplete topology anyhow, use the option -missingWith the actual Gromacs Error being:
Making bonds...
atom H26 is missing in residue GK2 1 in the pdb file
You might need to add atom H26 to the hydrogen database of building block GK2 in the file GK2.hdb (see the manual)
atom H27 is missing in residue GK2 1 in the pdb file...I understand this is an issue of a missing file from CGenFF, given that there is no GK2.hdb provided in the charmm36.ff directory, but how should I go about solving this?
Thanks for your help.
Hi @Patricio ,
Did the ligand structure that you submitted to CGenFF have all the necessary hydrogens?
For now, unfortunately, we don't yet have a GROMACS Wizard tutorial dedicated to the protein-ligand complex simulation with ligands parametrized using CGenFF. You can try to follow the corresponding steps from Justin Lemkul's Protein-ligand complex tutorial to obtain the ligand structure file and .itp file. You can add hydrogens in SAMSON, but the ligand needs to have charges and aromatic rings specified (it depends on the input file format).
Then you can combine the protein with the ligand structure directly in SAMSON. If needed, you can use Move editors to place the ligand, or the AutoDock Vina Extended to dock the ligand into a pocket. After that, you can follow the GROMACS Wizard tutorial with providing the generated .itp file and force field.If you'd like, you can send us (via contact@samson-connect.net) an archive of your system (excluding the protein, if desired) to test and identify the issue.
Dmitriy,
The SAMSON Team, https://s-c.io -
Hi @Patricio ,
Did the ligand structure that you submitted to CGenFF have all the necessary hydrogens?
For now, unfortunately, we don't yet have a GROMACS Wizard tutorial dedicated to the protein-ligand complex simulation with ligands parametrized using CGenFF. You can try to follow the corresponding steps from Justin Lemkul's Protein-ligand complex tutorial to obtain the ligand structure file and .itp file. You can add hydrogens in SAMSON, but the ligand needs to have charges and aromatic rings specified (it depends on the input file format).
Then you can combine the protein with the ligand structure directly in SAMSON. If needed, you can use Move editors to place the ligand, or the AutoDock Vina Extended to dock the ligand into a pocket. After that, you can follow the GROMACS Wizard tutorial with providing the generated .itp file and force field.If you'd like, you can send us (via contact@samson-connect.net) an archive of your system (excluding the protein, if desired) to test and identify the issue.
We have posted a brief tutorial on preparing protein-ligand systems with GROMACS Wizard. We will add more information to it over time, specific to each parametrization tool/server.
Hello! It looks like you're interested in this conversation, but you don't have an account yet.
Getting fed up of having to scroll through the same posts each visit? When you register for an account, you'll always come back to exactly where you were before, and choose to be notified of new replies (either via email, or push notification). You'll also be able to save bookmarks and upvote posts to show your appreciation to other community members.
With your input, this post could be even better 💗
Register Login