Dear Case,
Let me first describe what I have done till now, and then I will give the
error message I am getting:
I have created a new residue, named RC1, which is a cytosine molcule with
2 dummy atoms in it. The atom types I have used are the ones used in RC
residue of leaprc.ff99. RED protocol is used to find the RESP charges. For
the dummy atoms (DH1 and DH2), I have used 'DU' as the atom type.
Then, in xleap, I am doing the following:
----------------------------------------------------------------------
> source leaprc.ff99
----- Source: /programs/amber8/dat/leap/cmd/leaprc.ff99
----- Source of /programs/amber8/dat/leap/cmd/leaprc.ff99 done
Log file: ./leap.log
Loading parameters: /programs/amber8/dat/leap/parm/parm99.dat
Loading library: /programs/amber8/dat/leap/lib/all_nucleic94.lib
Loading library: /programs/amber8/dat/leap/lib/all_amino94.lib
Loading library: /programs/amber8/dat/leap/lib/all_aminoct94.lib
Loading library: /programs/amber8/dat/leap/lib/all_aminont94.lib
Loading library: /programs/amber8/dat/leap/lib/ions94.lib
Loading library: /programs/amber8/dat/leap/lib/solvents.lib
> loadoff cyto.lib
Loading library: ./cyto.lib
> new_cyto = loadpdb new_c_rc1.pdb
Loading PDB file: ./new_c_rc1.pdb
total atoms in file: 32
> saveamberparmpert new_cyto cyto_rc1_pert.top cyto_rc1_pert.crd
Checking Unit.
ERROR: The unperturbed charge of the unit: -1.297000 is not integral.
WARNING: The unperturbed charge of the unit: -1.297000 is not zero.
-- ignoring the error and warning.
Building topology.
Building atom parameters.
For atom: .R<C 14>.A<DH1 31> Could not find type: DU
For atom: .R<C 14>.A<DH2 32> Could not find type: DU
Parameter file was not saved.
--------------------------------------------------------------------
Does that mean that there is no dummy atom type defined in leaprc.ff99? If
not, how should I define it? Creating an frcmod file? Thanks in advance.
On Wed, 5 Jan 2005, David A. Case wrote:
> On Tue, Jan 04, 2005, Ilyas Yildirim wrote:
> >
> > > saveamberparm RC1 deneme.top deneme.crd
> > saveAmberParm: There are no parameter sets loaded
> >
> > If we create a .lib file, does not that include the parameters in them?
>
> No. Parameters are kept in a file like parm99.dat, or in a "frcmod" file
> (such as might be created by hand, or by antechamber).
>
> ...dac
>
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>
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
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- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Wed Jan 05 2005 - 21:53:00 PST
