6th May, 2021
Asked 31st May, 2018
How to solve Amber Leap PDB preparation error "atom does not have a type"?
I am using PDB file 5F9R of CRISPR/Cas9 pre-catalytic state structure for molecular dynamics simulation with AMBER. It is a complex of protein, DNA and RNA
First I ran the command:
pdb4amber -i 5f9r.pdb -o 5f9r_new.pdb --reduce --dry
then I used the following script to solvate the protein and add counter ions.
source leaprc.protein.ff14SB source leaprc.water.tip3p loadamberparams frcmod.ionsjc_tip3p crispr = loadpdb 5f9r_new.pdb solvatebox crispr TIP3PBOX 12.0 charge crispr addions2 crispr Cl- 0 saveamberparm crispr crispr.prmtop crispr.inpcrd quit But at the last step, the parameters cannot be saved because of this kind of errors:
FATAL: Atom .R<DG 1535>.A<C4 22> does not have a type.
It seems that the certain names of atoms in PDB file cannot be recognized by LEAP. I think this is caused by the atoms on DNA chain in the structure. (DG, DA, DT, DC are names of basic groups in DNA)
How can this problem be solved?
Thank you for your help.
Most recent answer
All Answers (8)
Sorry, I have checked the text file, and the problem is solved.
Now the fatal error of "DA, DG, DC, DT" and "A,G,C,U" not have type does not occur any more.
This is because that ff14SB is a "protein-only" force field. If we would like to include DNA and RNA we should source "leaprc.DNA.bsc1" and "leaprc.RNA.OL3" force fields.
Thank you for your help and suggestions!
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