Sorry for not being detail. I attach the message in the screen in Xleap:
> loadpdb 60-new.pdb
Loading PDB file: ./60-new.pdb
Unknown residue: NO_ number: 0 type: Terminal/last
...relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: NO_ sequence: 1
Created a new atom named: O_3 within residue: .R<NO_ 1>
Created a new atom named: HO_3 within residue: .R<NO_ 1>
Created a new atom named: C_3 within residue: .R<NO_ 1>
Created a new atom named: H_3 within residue: .R<NO_ 1>
Created a new atom named: C_2 within residue: .R<NO_ 1>
Created a new atom named: H_2 within residue: .R<NO_ 1>
Created a new atom named: O_2 within residue: .R<NO_ 1>
Created a new atom named: HO_2 within residue: .R<NO_ 1>
Created a new atom named: C_4 within residue: .R<NO_ 1>
Created a new atom named: H_4 within residue: .R<NO_ 1>
Created a new atom named: O_4 within residue: .R<NO_ 1>
Created a new atom named: HO_4 within residue: .R<NO_ 1>
Created a new atom named: C_5 within residue: .R<NO_ 1>
Created a new atom named: H_5 within residue: .R<NO_ 1>
Created a new atom named: C_6 within residue: .R<NO_ 1>
Created a new atom named: H_62 within residue: .R<NO_ 1>
Created a new atom named: H_61 within residue: .R<NO_ 1>
Created a new atom named: O_6 within residue: .R<NO_ 1>
Created a new atom named: HO_6 within residue: .R<NO_ 1>
Created a new atom named: O_5 within residue: .R<NO_ 1>
Created a new atom named: C_1 within residue: .R<NO_ 1>
Created a new atom named: H_1 within residue: .R<NO_ 1>
Created a new atom named: O_1 within residue: .R<NO_ 1>
Created a new atom named: C2 within residue: .R<NO_ 1>
Created a new atom named: H2 within residue: .R<NO_ 1>
Created a new atom named: C3 within residue: .R<NO_ 1>
Created a new atom named: H3 within residue: .R<NO_ 1>
Created a new atom named: O3 within residue: .R<NO_ 1>
Created a new atom named: HO3 within residue: .R<NO_ 1>
Created a new atom named: C4 within residue: .R<NO_ 1>
Created a new atom named: H4 within residue: .R<NO_ 1>
Created a new atom named: O4 within residue: .R<NO_ 1>
Created a new atom named: HO4 within residue: .R<NO_ 1>
Created a new atom named: C5 within residue: .R<NO_ 1>
Created a new atom named: H5 within residue: .R<NO_ 1>
Created a new atom named: C6 within residue: .R<NO_ 1>
Created a new atom named: H62 within residue: .R<NO_ 1>
Created a new atom named: H61 within residue: .R<NO_ 1>
Created a new atom named: O6 within residue: .R<NO_ 1>
Created a new atom named: HO6 within residue: .R<NO_ 1>
Created a new atom named: O5 within residue: .R<NO_ 1>
Created a new atom named: C1 within residue: .R<NO_ 1>
Created a new atom named: H1 within residue: .R<NO_ 1>
Created a new atom named: O1 within residue: .R<NO_ 1>
Created a new atom named: HO1 within residue: .R<NO_ 1>
total atoms in file: 45
The file contained 45 atoms not in residue templates
But 60-new.pdb is the one I used prmtop & inpcrd files to get. I still cannot
load it. Did I miss anything? Thank you for reply.
Lan
Quoting "David A. Case" <case.scripps.edu>:
> On Wed, Dec 31, 2003, L Jin wrote:
>
> > But I tried this ambpdb command as following:
> >
> > ambpdb -p 60.prmtop < restrt > new.pdb
> >
> > But I still cannot use loadpdb command to load it to the leap. Anybody can
> > help me?
>
> We can only help if you provide more information. What happens when you
> try to use the loadpdb command? Just saying "it doesn't work" is not very
> helpful (to you, or to us). Look carefully at any messages you get, either
> on the screen or in the leap.log file.
>
> ..good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case.scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
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Received on Wed Jan 14 2004 - 15:53:13 PST
