I edited the pdb file,but another problem appeared. it reads like this:
> mol = loadpdb wt1mg_water.pdb
Loading PDB file: ./wt1mg_water.pdb
Created a new atom named: H within residue: .R<NCYS 1>
total atoms in file: 2381
Leap added 3 missing atoms according to residue templates:
3 H / lone pairs
The file contained 1 atoms not in residue templates
> saveAmberParm mol wt1mg_dry.parm7 wt1mg_dry.rst
Checking Unit.
WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
FATAL: Atom .R<NCYS 1>.A<H 14> does not have a type.
Failed to generate parameters
Parameter file was not saved.
I have attached my pdb file to this email. I really didn't get into this
thing. Thx~`
2010/4/24 Bill Ross <ross.cgl.ucsf.edu>
> > It's not clear how you created the "wt1mg_water.pdb" file, but it is easy
> > enough to examine it to see if there are duplicate H atoms in residue 1.
> They
> > probably won't cause any problem.
>
> I think you will have to delete one of the duplicates before loadpdb
> in order to get saveamberparm to work.
>
> Bill
>
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Received on Tue May 04 2010 - 02:30:04 PDT
