AMBER Archive (2004)

Subject: Re: AMBER: Antechamber & Ptraj/Rdparm

From: zhaoxc_at_puccini.che.pitt.edu
Date: Thu Jan 01 2004 - 09:05:31 CST

On Thu, 1 Jan 2004, L Jin wrote:

> 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

did you modify the pdb file (specifically the residue name) manually? here
leap doesnot recognize the residue name.

> ..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_at_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_at_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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>
>
>
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