Your pdb file has already been edited (by Maestro, according to the header)
and now it has has non standard names for hydrogen atoms. You can either
use the original pdb file from RCSB, and allow leap to add H atoms with
correct names, or you can try to see if pdb4amber can fix these names
before using leap.
On Tue, Mar 29, 2022, 3:04 AM Debasish Mandal <debu1500.gmail.com> wrote:
> Hello Amber users,
> I am a beginner of amber. I am trying to
> prepare the parameter file for a protein in AMBER. Unfortunately it gives
> an error and shows "Leap added 411 missing atoms according to residue
> templates:" The leap.log file and pdb are attached herewith. Any help will
> be appreciated to solve this problem.
>
> Thanks & Regards
> Debasish
> ======================================
>
>
> *Dr. Debasish Mandal *
> *Assistant Professor*
> *School of Chemistry and Biochemistry*
> *Thapar Institute of Engineering and Technology, *
> *Patiala - 147004, Punjab, India**Mobile No: +918017296958*
>
>
>
> “I’m thankful to all those who said ‘NO’ to me it's because of them, I did
> it
>
> myself” Einstein
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>
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Received on Tue Mar 29 2022 - 04:00:03 PDT
