Question
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

Some times I just remove the atoms that not have a type from the initial PDB mannualy and run again the Leap.
Because the Leap adds correctly the missing atmos.

All Answers (8)

31st May, 2018
Yoshinobu Ishikawa
Shonan University of Medical Sciences
Hi Zhehan,
Did you source force fileds for DNA and RNA like leaprc.DNA.bsc1 and leaprc.RNA.OL3?
31st May, 2018
Zhehan Fu
Peking University
I have tried to source these two force fields but after then I ran "check" the structure and the problem still existed
1st Jun, 2018
Yoshinobu Ishikawa
Shonan University of Medical Sciences
Try if other pdb structures of protein/nucleic acid complex work fine.
1st Jun, 2018
Yoshinobu Ishikawa
Shonan University of Medical Sciences
You should list if DG, DA, DT, and DC parameters have been loaded in leap.
1st Jun, 2018
Zhehan Fu
Peking University
I have run "list" in tleap after loading DNA, RNA and protein force fields. And it showed that DA, DG, DC, DT and A/U/G/C are all loaded in leap. But the "does not have type" error still exists.
1st Jun, 2018
Yoshinobu Ishikawa
Shonan University of Medical Sciences
Did you check the atoms of DG, DT, ··· in the text file and visually?
1st Jun, 2018
Zhehan Fu
Peking University
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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