[AMBER] Request of help on Leap PDB preparation error "atom does not have a type"

From: 符哲瀚 <frederick.fu.pku.edu.cn>
Date: Wed, 30 May 2018 12:32:33 +0800 (GMT+08:00)

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

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

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Received on Tue May 29 2018 - 22:00:03 PDT
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