Hi all,
I would like to correctly prepare a capped protein (N-terminal acetyl and C-terminal N-Me amide capping groups)
I have prepared the protein using MOE and conform the name to AMBER format.
Do you know how to resolve the issue? Or where in the manual or related documents can I fix the issues?
I am using Amber18
> mol=loadPDB 4yzc_restrained_miminization_only_protein_AMBER_format.pdb
Loading PDB file: ./4yzc_restrained_miminization_only_protein_AMBER_format.pdb
Warning: Unknown residue: NMA number: 403 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Warning: Unknown residue: NMA number: 807 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Created a new atom named: HH31 within residue: .R<ACE 0>
Created a new atom named: HH32 within residue: .R<ACE 0>
Created a new atom named: HH33 within residue: .R<ACE 0>
Creating new UNIT for residue: NMA sequence: 403
Warning: One sided connection. Residue () missing connect0 atom.
Created a new atom named: N within residue: .R<NMA 403>
Created a new atom named: CA within residue: .R<NMA 403>
Created a new atom named: H within residue: .R<NMA 403>
Created a new atom named: HA1 within residue: .R<NMA 403>
Created a new atom named: HA2 within residue: .R<NMA 403>
Created a new atom named: HA3 within residue: .R<NMA 403>
Created a new atom named: HH31 within residue: .R<ACE 404>
Created a new atom named: HH32 within residue: .R<ACE 404>
Created a new atom named: HH33 within residue: .R<ACE 404>
Creating new UNIT for residue: NMA sequence: 807
Warning: One sided connection. Residue () missing connect0 atom.
Created a new atom named: N within residue: .R<NMA 807>
Created a new atom named: CA within residue: .R<NMA 807>
Created a new atom named: H within residue: .R<NMA 807>
Created a new atom named: HA1 within residue: .R<NMA 807>
Created a new atom named: HA2 within residue: .R<NMA 807>
Created a new atom named: HA3 within residue: .R<NMA 807>
total atoms in file: 13022
Leap added 6 missing atoms according to residue templates:
6 H / lone pairs
The file contained 18 atoms not in residue templates
Thank you!
Antonio
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 19 2018 - 00:00:02 PDT
