I want to perform a protein-ligand MD simulation using Amber. I have generated ligand frcmod, lib, rst7, and prmtop files. Then, I loaded my complex file, which contained the ligand and protein in water (generated using Packmol-memgen). However, when I tried to save the rst7 and prmtop files for the complex, I encountered this error: 'FATAL: Atom .R does not have a type.' I've attempted to resolve this issue multiple times, but it keeps happening. I followed the tutorial exactly as outlined on the AmberMD website ('Simulating a pharmaceutical compound using Antechamber and the Generalized Amber Force Field'). Surprisingly, the problem persists. even though I tried to use the same molecule, protein, and files provided on the website to check out if there were any problem with my own files and again i ended up with same problem. Can anyone help me figure this out?"
This error typically occurs when the atom names provided in the pdb file that you are using to generate the topology do not match the (unique) atom names contained in the off file. As a consequence, tleap is not able to assign to the atoms in the pdb the correct atom type, connectivity, and partial charges. To solve the problem, just rename the pdb atoms according to the naming that appears in the "unit.atoms table" section of the off file. The same error may arise also if there is a mismatch between the three-letter residue name between pdb and off file. The solution in that case is to change the pdb residue name to the one that appears in the "index array str" section of the off file.
Hi! The tutorial you mentioned on AMBER website consists of "sustiva" as the ligand which has been named as "SUS" in tleap. Thus, make sure that the residue name besides the atoms of the ligand in the protein-ligand complex is "SUS" too.
Hi, I also encountered the same error while generating prmtop and rst7 for the complex, but when I loaded the complex pdb file, some new atoms were added by the tleap in the pdb file. Is there a solution to deal with the error ?
>complex = loadpdb protein_mol.pdb
Loading PDB file: ./protein_mol.pdb
Created a new atom named: H within residue: .R
Created a new atom named: HD1 within residue: .R
Created a new atom named: HD1 within residue: .R
Created a new atom named: HD1 within residue: .R
total atoms in file: 2928
Leap added 5 missing atoms according to residue templates:
5 H / lone pairs
The file contained 4 atoms not in residue templates
> saveamberparm complex protein_mol.prmtop protein_mol.rst7
Checking Unit.
Warning: The unperturbed charge of the unit (1.999000) is not zero.
FATAL: Atom .R.A does not have a type.
FATAL: Atom .R.A does not have a type.
FATAL: Atom .R.A does not have a type.
FATAL: Atom .R.A does not have a type.
Error: Failed to generate parameters
Warning: Parameter file was not saved.
Hi,
did you find a solution? I'm in a similar situation with the same kind of error
Thanks,
Marco
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