I am using PDB file 5F9R of CRISPR/Cas9 pre-catalytic state structure for molecular dynamics simulation. 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.
Fu Zhehan
Peking University Undergraduate
Major: Biomedical Engineering,Department Biomedical Engineering, College of Engineering, Peking University
Research Assistant, Brain-like Computing Group, Digital Media Institute, Peking University
Student ID: 1500011037
Tel: (+86) 15600931838
Room No. 417,Building 29, Peking University, No.5 Yiheyuan Road, Haidian District, Bejing, ChinaPR
100871
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Received on Tue May 29 2018 - 22:00:03 PDT
