Hi,
I was unable to reproduce your error, but I was able to successfully
generate a topology file using pdb 1atp with the exact same ATP parameters
you used from the Bryce group. Try (1) changing the residue name of 'ATP'
to 'atp' in the pdb file to match the prep file if you haven't already, and
(2) sourcing a DNA force field before loading in the pdb with atp. I was
only able to generate a parameter file if I did those two steps.
Hope that helps,
--Zachary
On Wed, Jul 10, 2019 at 10:52 AM 李耀 <liyao17.mails.tsinghua.edu.cn> wrote:
> Dear Amber users,
>
>
> I used the force field parameter of Bryce group(
> http://research.bmh.manchester.ac.uk/bryce/amber) to generate topology
> file for a protein-ATP complex. I saved the PREP and FRCMOD as atp.prep
> and frcmod.atp. Here is the tleap command:
>
>
> source leaprc.protein.ff14SB
> loadamberparams frcmod.atp
> loadamberprep atp.prep
>
>
> mol = loadpdb c-src-atp.pdb
> saveamberparm mol c-src-atp.prmtop c-src-atp.inpcrd
>
>
> And the leap reported the following error:
>
>
> Error: Could not find bond parameter for: C - O3
> Building angle parameters.
>
>
> Error: Could not find angle parameter: O - C - O3
>
>
> Error: Could not find angle parameter: C - O3 - P
>
>
> Error: Could not find angle parameter: CX - C - O3
> Building proper torsion parameters.
>
>
> Error: ** No torsion terms for O-C-O3-P
>
>
> Error: ** No torsion terms for C-O3-P-O3
>
>
> Error: ** No torsion terms for C-O3-P-O3
>
>
> Error: ** No torsion terms for C-O3-P-OS
>
>
> Error: ** No torsion terms for CX-C-O3-P
> Building improper torsion parameters.
> old PREP-specified impropers:
> <atp 522>: C8 C4 N9 C1*
> <atp 522>: C6 H60 N6 H61
> <atp 522>: N7 N9 C8 H80
> <atp 522>: N1 N3 C2 H2
> <atp 522>: C5 N1 C6 N6
> total 849 improper torsions applied
> 5 improper torsions in old prep form
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
>
>
> Warning: Parameter file was not saved.
>
>
> The structure of ATP in my pdb file is exactly the same as that in PKA
> kinase (PDB 1ATP). I think I didn't use the force field parameter file
> correctly. Could you please tell me how to do with this? Thank you!
>
>
> Best,
> Yao Li
>
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Zachary Fallon, PhD Candidate
Dr. Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (914) 703-1010 <(914)+703+1010> Email: zachary.fallon.stonybrook.
<zachary.fallon.stonybrook.edu>edu
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Received on Wed Jul 10 2019 - 10:00:04 PDT
