AMBER Archive (2003)

Subject: Re: AMBER

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 15 2003 - 19:38:59 CDT

On Tue, Apr 15, 2003, chandran karunakaran wrote:
> Dear AMBER users,
> I am interested in molecular dynamics of
> mutant copper proteins. Before I do that,
> I tried with plastocyanin. Thanks for
> correcting me to include Cu in HIC
> residue. Afterwards I ran and got this
> output. Could any one suggest me what
> should I do? Sorry for disturbance.
>
>
> Welcome to LEaP!
> Sourcing leaprc:
> /home/amkumar/soft/amber6/dat/leap/cmd/leaprc
> Log file: ./leap.log
> Loading parameters:
> /home/amkumar/soft/amber6/dat/parm94.dat
> Loading library:
> /home/amkumar/soft/amber6/dat/leap/lib/all_nucleic94.lib
> Loading library:
> /home/amkumar/soft/amber6/dat/leap/lib/all_amino94.lib
> Loading library:
> /home/amkumar/soft/amber6/dat/leap/lib/all_aminoct94.lib
> Loading library:
> /home/amkumar/soft/amber6/dat/leap/lib/all_aminont94.lib
> Loading library:
> /home/amkumar/soft/amber6/dat/leap/lib/ions94.lib
> Loading library:
> /home/amkumar/soft/amber6/dat/leap/lib/water.lib
> Sourcing: ./leapp.in
> Loading parameters: ./frcmodp.pcy
> Reading force field mod type file (frcmod)
> Loading Prep file: ./mem.in
> Loading Prep file: ./hicu.in
> Loading PDB file: ./1plc.H.pdb
> Added missing heavy atom: .R<HIC 100>.A<N 1>
> Added missing heavy atom: .R<HIC 100>.A<CA 3>
> Added missing heavy atom: .R<HIC 100>.A<CB 5>
> Added missing heavy atom: .R<HIC 100>.A<C 17>
> Added missing heavy atom: .R<HIC 100>.A<CG 8>
> Added missing heavy atom: .R<HIC 100>.A<O 18>
> Added missing heavy atom: .R<HIC 100>.A<ND1 9>
> Added missing heavy atom: .R<HIC 100>.A<CD2 15>
> Added missing heavy atom: .R<HIC 100>.A<CE1 11>
> Added missing heavy atom: .R<HIC 100>.A<NE2 13>
> total atoms in file: 1442

If you are using poplar plastocyanin, (1plc.pdb) there should only be 99
residues...you need to figure out why LEaP thinks that residue 100 is "HIC".
That should be fairly obvious if you carefully examine your pdb file.
[In general, if LEaP is complaining about residue 100, and there are only 99
residues in your protein, you need to examine the input pdb file carefully
to try to figure out what is going on.]

Also, be sure that your residue 37 is named HIC, and that your residue
92 is named MEM, as stated in the tutorial instructions.

It looks to me like the problems are all related to what is in your file
called "1plc.H.pdb". If necessary, send that file along with future
questions. But, please, try to fix the things above yourself...that is the
only way to learn.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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