just a quick note on this, leap is not a particularly demanding
application, you should be able to run it easily on any personal computer
with unix, and therefore you could use xleap.
On Thu, Oct 18, 2012 at 11:07 PM, Changqing Yan <ycqchemical.gmail.com>wrote:
> Dear Sir,
>
> Thanks for your replies before.
>
> I try to create my non-standard residue such as N-methylatd valine
> according to the tutorial
> http://ambermd.org/tutorials/advanced/tutorial1/section3.htm. However,
> when
> I proceed to this step *3.1.1) Defining the FAM5 Topology . I load my pdb
> into leap. Before loading, the pdb seems ok. But after loading, it displays
>
> > nme = loadpdb nme-valine-resp-modified.pdb
> Loading PDB file: ./nme-valine-resp-modified.pdb
> Unknown residue: NMe number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: NMe sequence: 1
> Created a new atom named: N1 within residue: .R<NMe 1>
> Created a new atom named: C1 within residue: .R<NMe 1>
> Created a new atom named: H1 within residue: .R<NMe 1>
> Created a new atom named: C2 within residue: .R<NMe 1>
> Created a new atom named: C3 within residue: .R<NMe 1>
> Created a new atom named: H2 within residue: .R<NMe 1>
> Created a new atom named: C4 within residue: .R<NMe 1>
> Created a new atom named: C5 within residue: .R<NMe 1>
> Created a new atom named: O1 within residue: .R<NMe 1>
> Created a new atom named: H3 within residue: .R<NMe 1>
> Created a new atom named: H4 within residue: .R<NMe 1>
> Created a new atom named: H5 within residue: .R<NMe 1>
> Created a new atom named: H6 within residue: .R<NMe 1>
> Created a new atom named: H7 within residue: .R<NMe 1>
> Created a new atom named: H8 within residue: .R<NMe 1>
> Created a new atom named: C6 within residue: .R<NMe 1>
> Created a new atom named: H9 within residue: .R<NMe 1>
> Created a new atom named: H10 within residue: .R<NMe 1>
> Created a new atom named: H11 within residue: .R<NMe 1>
> total atoms in file: 19
> The file contained 19 atoms not in residue templates
>
> It is like the tutorial. However, when I check the nme unit, it displays.
>
> > check nme
> Checking 'nme'....
> FATAL: Atom .R<NMe 1>.A<N1 1> does not have a type.
> FATAL: Atom .R<NMe 1>.A<C1 2> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H1 3> does not have a type.
> FATAL: Atom .R<NMe 1>.A<C2 4> does not have a type.
> FATAL: Atom .R<NMe 1>.A<C3 5> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H2 6> does not have a type.
> FATAL: Atom .R<NMe 1>.A<C4 7> does not have a type.
> FATAL: Atom .R<NMe 1>.A<C5 8> does not have a type.
> FATAL: Atom .R<NMe 1>.A<O1 9> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H3 10> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H4 11> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H5 12> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H6 13> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H7 14> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H8 15> does not have a type.
> FATAL: Atom .R<NMe 1>.A<C6 16> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H9 17> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H10 18> does not have a type.
> FATAL: Atom .R<NMe 1>.A<H11 19> does not have a type.
> Warning: Close contact of 2.000000 angstroms between .R<NMe 1>.A<N1 1> and
> .R<NMe 1>.A<O1 9>
> Warning: Close contact of 1.036100 angstroms between .R<NMe 1>.A<C2 4> and
> .R<NMe 1>.A<H5 12>
> Warning: Close contact of 2.072900 angstroms between .R<NMe 1>.A<C3 5> and
> .R<NMe 1>.A<H6 13>
> Warning: Close contact of 1.166400 angstroms between .R<NMe 1>.A<C3 5> and
> .R<NMe 1>.A<H7 14>
> Warning: Close contact of 0.562500 angstroms between .R<NMe 1>.A<H3 10> and
> .R<NMe 1>.A<H7 14>
> Checking parameters for unit 'nme'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Errors: 19 Warnings: 5
>
> The coordinates seems not correct at this time. What happened exactly? And
> what should I do? Besides, the tutorial use a xleap, I can only use tleap
> in my nodes. How can proceed to the next step, ie. to conncet the atoms and
> assign them charges?
>
> Thanks.
> C.Q.
> *
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Oct 18 2012 - 21:30:03 PDT
