?Hi everyone,
Please guide me what is the command to generate the top and crd file once I
generated the frcmod and prepin files.
In the command
> saveamberparm DRG ligand.prmtop ligand.inpcrd
The DRG = loadpdb pdb1_10854218DOCK.pdb
But when I load the DRG with the protein ligand complex it is giving:
Loading PDB file: ./pdb1_10854218DOCK.pdb
Unknown residue: DRG number: 212 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Created a new atom named: OXT within residue: .R<CYS 212>
Creating new UNIT for residue: DRG sequence: 213
One sided connection. Residue: missing connect0 atom.
Created a new atom named: C within residue: .R<DRG 213>
Created a new atom named: H within residue: .R<DRG 213>
Created a new atom named: H1 within residue: .R<DRG 213>
Created a new atom named: H2 within residue: .R<DRG 213>
Created a new atom named: C1 within residue: .R<DRG 213>
Created a new atom named: H3 within residue: .R<DRG 213>
Created a new atom named: H4 within residue: .R<DRG 213>
Created a new atom named: O within residue: .R<DRG 213>
Created a new atom named: C2 within residue: .R<DRG 213>
Created a new atom named: O1 within residue: .R<DRG 213>
Created a new atom named: C3 within residue: .R<DRG 213>
Created a new atom named: C29 within residue: .R<DRG 213>
Created a new atom named: N3 within residue: .R<DRG 213>
Created a new atom named: C4 within residue: .R<DRG 213>
Created a new atom named: H5 within residue: .R<DRG 213>
Created a new atom named: C5 within residue: .R<DRG 213>
Created a new atom named: C10 within residue: .R<DRG 213>
Created a new atom named: C9 within residue: .R<DRG 213>
Created a new atom named: H8 within residue: .R<DRG 213>
Created a new atom named: H9 within residue: .R<DRG 213>
Created a new atom named: C6 within residue: .R<DRG 213>
Created a new atom named: H6 within residue: .R<DRG 213>
Created a new atom named: C7 within residue: .R<DRG 213>
Created a new atom named: H7 within residue: .R<DRG 213>
Created a new atom named: C8 within residue: .R<DRG 213>
Created a new atom named: N within residue: .R<DRG 213>
Created a new atom named: C14 within residue: .R<DRG 213>
Created a new atom named: C13 within residue: .R<DRG 213>
Created a new atom named: H14 within residue: .R<DRG 213>
Created a new atom named: H15 within residue: .R<DRG 213>
Created a new atom named: H16 within residue: .R<DRG 213>
Created a new atom named: H17 within residue: .R<DRG 213>
Created a new atom named: C11 within residue: .R<DRG 213>
Created a new atom named: H10 within residue: .R<DRG 213>
Created a new atom named: H11 within residue: .R<DRG 213>
Created a new atom named: C12 within residue: .R<DRG 213>
Created a new atom named: H12 within residue: .R<DRG 213>
Created a new atom named: H13 within residue: .R<DRG 213>
Created a new atom named: N1 within residue: .R<DRG 213>
Created a new atom named: C15 within residue: .R<DRG 213>
Created a new atom named: H18 within residue: .R<DRG 213>
Created a new atom named: H19 within residue: .R<DRG 213>
Created a new atom named: C16 within residue: .R<DRG 213>
Created a new atom named: H20 within residue: .R<DRG 213>
Created a new atom named: H21 within residue: .R<DRG 213>
Created a new atom named: N2 within residue: .R<DRG 213>
Created a new atom named: C28 within residue: .R<DRG 213>
Created a new atom named: O3 within residue: .R<DRG 213>
Created a new atom named: C17 within residue: .R<DRG 213>
Created a new atom named: O2 within residue: .R<DRG 213>
Created a new atom named: C18 within residue: .R<DRG 213>
Created a new atom named: C19 within residue: .R<DRG 213>
Created a new atom named: H22 within residue: .R<DRG 213>
Created a new atom named: C20 within residue: .R<DRG 213>
Created a new atom named: H23 within residue: .R<DRG 213>
Created a new atom named: C21 within residue: .R<DRG 213>
Created a new atom named: H24 within residue: .R<DRG 213>
Created a new atom named: C22 within residue: .R<DRG 213>
Created a new atom named: C23 within residue: .R<DRG 213>
Created a new atom named: C24 within residue: .R<DRG 213>
Created a new atom named: C25 within residue: .R<DRG 213>
Created a new atom named: H25 within residue: .R<DRG 213>
Created a new atom named: C26 within residue: .R<DRG 213>
Created a new atom named: H26 within residue: .R<DRG 213>
Created a new atom named: C27 within residue: .R<DRG 213>
Created a new atom named: H27 within residue: .R<DRG 213>
total atoms in file: 3493
The file contained 67 atoms not in residue templates
*Please help me with how to proceed with making top and crd files, after I
generated the prepin and frcmod files.*
Thanking for your valuable time and guidance.
Best Regards,
Ruchika
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Received on Fri Nov 07 2014 - 06:00:03 PST
