hi i have run pdb2gmx for protein topology and the error is coming for hydrogen. I don’t know if -ignh flag should be used or not
End terminus HIS-525: COO-
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn
-------------------------------------------------------
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790)
Fatal error:
Atom HD1 in residue HIS 20 was not found in rtp entry HSE with 17 atoms
while sorting atoms.
For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
As mentioned in your error message add ignore hydrogens to your command, this may resolve the issue
gmx pdb2gmx -f input.pdb -o output.gro -water spce -ignh
When working with PDB files, especially those from NMR structures, it’s often more convenient to disregard hydrogen (H) atoms. This is because, if hydrogen atoms are included, they need to be named exactly as specified by the force fields in GROMACS. Since naming conventions for hydrogen atoms vary, this can sometimes cause complications. If you want to keep the original coordinates of hydrogen atoms but need to rename them, the sed command in Linux can be a useful tool for this purpose.
If the protein is modeled, the positions of the H atoms are the least concerning consideration in whether or not the model is reasonable. Use -ignh and reconstruct them with the appropriate names.
i used a protein-ligand complex after getting it from autodockVina i.e after docking. The ligand bound with this protein is designed by me. I did docking and after that i got the complex with best score. Then i input in gromacs. My question is that whether i need to process it again by removing water and het atom? And i also got an error like this
“For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.”
please help, iam new to this
Quiero hacer una MD ligando-proteína. A la proteína le he asignado los estados de protonación pH ácido, con la herramienta Charmm Gui y al ligando con CGENFF. Al crear la topología con campo de fuerza charmm32 con el comando gmx pdb2gmx -f input.pdb -o output.gro -water spce, todo funciona bien, ya que estoy trabajando en todo momento con el mismo campo de fuerza Charmm. Pero quiero trabajar la proteína ahora con un campo de fuerza OPLS-AA, ya que mi ligando esta vez maneja un campo de fuerza generado con PolyParGen y aquí ya presentó el problema con los hidrógenos asignados en la protonación. Mis preguntas son:
si utilizo -ignh, Gromacs arregla los nombres o asigna los hidrógenos a un pH 7 o que es lo que hace?
Qué herramienta puedo usar para protonar una proteína que contenga los parámetros de la topología OPLS-AA o qué puedo hacer con Gromacs?
I want to make a ligand-protein MD. I have assigned the protein the acidic pH protonation states, with the Charmm Gui tool and the ligand with CGENFF. When creating the topology with the charmm32 force field with the gmx command pdb2gmx -f input.pdb -or output.gro -water spce, everything works fine, as I am working always with the same Charmm force field. But now I want to work the protein with an OPLS-AA force field, since my ligand this time handles a force field generated with PolyParGen and here the problem with the hydrogens assigned in the protonation already occurred. My questions are:
if I use -ignh, does Gromacs fix the names or assign the hydrogens at pH 7 or what does it do?
What tool can I use to protonate a protein containing the OPLS-AA topology parameters or what can I do with Gromacs?