I am trying to run MD calculations with an RNA aptamer in Amber. The first step (detachement of hydrogens) occurs fine:
pdb4amber -y -i 7kd1.pdb -o apt-nh.pdb
However, this command gives the message:
"The following residues had alternate locations: U_21"
Than, I go with a command @tleap -f leaprc.RNA.OL3@ which works fine.
Than I print:
rec=loadpdb apt-nh.pdb
which results in:
Created a new atom named: P within residue: .R
Created a new atom named: OP1 within residue: .R
Created a new atom named: OP2 within residue: .R
Created a new atom named: OP3 within residue: .R
total atoms in file: 1914
Leap added 961 missing atoms according to residue templates:
961 H / lone pairs
The file contained 4 atoms not in residue templates
I type:
set default PBRadii mbondi2
Finally, I try to generate a topology file "saveamberparm rec apt.prmtop apt.inpcrd", which results in:
Warning: The unperturbed charge of the unit (-88.000000) 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.
However, when I look through the pdb file I cannot see abnormalities or missing atom types. So what is wrong with my pdb file (attached)?
It seems like the issue might be related to the naming of the atoms in your PDB file. The error message "Atom .R.A
does not have a type" suggests that the atom types are not recognized by the parameter files in Amber.
One common issue could be the naming convention used in the PDB file. Make sure that the atom names in your PDB file match the atom names expected by Amber. You can check the atom names in the parameter files provided by Amber and ensure that they match the atom names in your PDB file.
Additionally, it's possible that there might be some missing atom types or parameters in the force field files you are using. Double-check that you have loaded the correct force field parameters in tleap and that they include parameters for all the atom types in your system.
If you continue to encounter issues, you may want to check the atom names and types in your PDB file carefully, compare them with the force field parameters, and ensure they are consistent. You can also try visualizing your system in a molecular visualization software like CHARM GUI to check for any anomalies in atom names or types that might be causing the error.