Hi,
Please try the following commands in tleap:
source leaprc.gaff
loadamberprep DRG.prepin
loadamberparams DRG.frcmod
a = loadpdb complex.pdb
...
It would be more complicated if some bond- or anlge- or torsion-parameters are missing.
Anyway, you can follow the tutorial 4b.
Best,
Wei Ye, PhD Candidate
Department of Bioinformatics and Biostatistics,
School of Life Science,
Shanghai Jiaotong University,
800 Dongchuan RD, Shanghai, China.
Email: yw20055968.126.com
在2014年11月07 21时39分, "Ruchika Bhat"<ruchikabhat31.gmail.com>写道:
?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 - 06:30:03 PST
