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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Received on Thu Oct 18 2012 - 20:30:03 PDT
