Hello Amber Users,
I am trying to start QM/MM setup/simulation for already simulated system (H293S-Arg) using the cluster analysis pdb, cluster_4. I am currently at the developing parameters for the complex but have stumbled upon a slight problem. I ran this pdb (B4M_initial_str_cluster_9-SAM-fixed.pdb) through tleap and its giving me the following error:
See below for leap.log file:
> complex = loadpdb B4M_initial_str_cluster_4-SAM_fixed.pdb
Loading PDB file: ./B4M_initial_str_cluster_4-SAM_fixed.pdb
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
(Residue 0: ALA, Terminal/beginning, was not found in name map.)
Unknown residue: ALA number: 0 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
(Residue 1: GLU, Nonterminal, was not found in name map.)
Unknown residue: GLU number: 1 type: Nonterminal
(Residue 2: ASP, Nonterminal, was not found in name map.)
Unknown residue: ASP number: 2 type: Nonterminal
(Residue 3: MET, Nonterminal, was not found in name map.)
Unknown residue: MET number: 3 type: Nonterminal
(Residue 4: THR, Nonterminal, was not found in name map.)
Unknown residue: THR number: 4 type: Nonterminal
Skipping.....
Created a new atom named: HA within residue: .R<TYR 10>
Created a new atom named: CB within residue: .R<TYR 10>
Created a new atom named: HB2 within residue: .R<TYR 10>
Created a new atom named: HB3 within residue: .R<TYR 10>
Created a new atom named: CG within residue: .R<TYR 10>
Created a new atom named: CD1 within residue: .R<TYR 10>
Created a new atom named: HD1 within residue: .R<TYR 10>
Created a new atom named: CE1 within residue: .R<TYR 10>
Created a new atom named: HE1 within residue: .R<TYR 10>
Created a new atom named: CZ within residue: .R<TYR 10>
Created a new atom named: OH within residue: .R<TYR 10>
Created a new atom named: HH within residue: .R<TYR 10>
Created a new atom named: CE2 within residue: .R<TYR 10>
Created a new atom named: HE2 within residue: .R<TYR 10>
Created a new atom named: CD2 within residue: .R<TYR 10>
Created a new atom named: HD2 within residue: .R<TYR 10>
Created a new atom named: C within residue: .R<TYR 10>
Created a new atom named: O within residue: .R<TYR 10>
Creating new UNIT for residue: PHE sequence: 11
If you could, guide me in the right direction to fixing this problem?
Thank you in advance,
?
Brittany Boykin
Graduate Student
Auburn University
Department of Chemistry and Biochemistry
e: bzb0031.tigermail.auburn.edu
c: (404)545.1036
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Received on Fri May 22 2015 - 13:00:03 PDT
