Just a guess and please correct me if I’m wrong though if you are using a “newer” version you should probably source the bsc1 or ol15 forcefield since they contain DNA related data?
Best regards
// Gustaf
> On 30 May 2018, at 06:32, 符哲瀚 <frederick.fu.pku.edu.cn> wrote:
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 30 2018 - 00:00:02 PDT
