Hi all,
i'm new to amber and my pdb file contains inosine residues. On using
'loadpdb' command, leap complains the following:
Loading PDB file: ./inosine.pdb
Unknown residue: I number: 3 type: Nonterminal
Unknown residue: I number: 15 type: Nonterminal
Creating new UNIT for residue: I sequence: 4
One sided connection. Residue: missing connect0 atom.
Created a new atom named: P within residue: .R<I 4>
Created a new atom named: O1P within residue: .R<I 4>
Created a new atom named: O2P within residue: .R<I 4>
Created a new atom named: O5* within residue: .R<I 4>
Created a new atom named: C5* within residue: .R<I 4>
Created a new atom named: C4* within residue: .R<I 4>
Created a new atom named: O4* within residue: .R<I 4>
Created a new atom named: C3* within residue: .R<I 4>
Created a new atom named: O3* within residue: .R<I 4>
Created a new atom named: C2* within residue: .R<I 4>
Created a new atom named: C1* within residue: .R<I 4>
Created a new atom named: N9 within residue: .R<I 4>
Created a new atom named: C8 within residue: .R<I 4>
Created a new atom named: N7 within residue: .R<I 4>
Created a new atom named: C5 within residue: .R<I 4>
Created a new atom named: C6 within residue: .R<I 4>
Created a new atom named: O6 within residue: .R<I 4>
Created a new atom named: N1 within residue: .R<I 4>
Created a new atom named: C2 within residue: .R<I 4>
Created a new atom named: N3 within residue: .R<I 4>
Created a new atom named: C4 within residue: .R<I 4>
One sided connection. Residue: missing connect1 atom.
Creating new UNIT for residue: I sequence: 16
One sided connection. Residue: missing connect0 atom.
Created a new atom named: P within residue: .R<I 16>
Created a new atom named: O1P within residue: .R<I 16>
Created a new atom named: O2P within residue: .R<I 16>
Created a new atom named: O5* within residue: .R<I 16>
Created a new atom named: C5* within residue: .R<I 16>
Created a new atom named: C4* within residue: .R<I 16>
Created a new atom named: O4* within residue: .R<I 16>
Created a new atom named: C3* within residue: .R<I 16>
Created a new atom named: O3* within residue: .R<I 16>
Created a new atom named: C2* within residue: .R<I 16>
Created a new atom named: C1* within residue: .R<I 16>
Created a new atom named: N9 within residue: .R<I 16>
Created a new atom named: C8 within residue: .R<I 16>
Created a new atom named: N7 within residue: .R<I 16>
Created a new atom named: C5 within residue: .R<I 16>
Created a new atom named: C6 within residue: .R<I 16>
Created a new atom named: O6 within residue: .R<I 16>
Created a new atom named: N1 within residue: .R<I 16>
Created a new atom named: C2 within residue: .R<I 16>
Created a new atom named: N3 within residue: .R<I 16>
Created a new atom named: C4 within residue: .R<I 16>
One sided connection. Residue: missing connect1 atom.
total atoms in file: 552
Leap added 378 missing atoms according to residue templates:
378 H / lone pairs
The file contained 42 atoms not in residue templates
On using the 'check' command, i got the following output:
Checking 'model'....
WARNING: The unperturbed charge of the unit: -20.000000 is not zero.
FATAL: Atom .R<I 4>.A<P 1> does not have a type.
FATAL: Atom .R<I 4>.A<O1P 2> does not have a type.
FATAL: Atom .R<I 4>.A<O2P 3> does not have a type.
FATAL: Atom .R<I 4>.A<O5* 4> does not have a type.
FATAL: Atom .R<I 4>.A<C5* 5> does not have a type.
FATAL: Atom .R<I 4>.A<C4* 6> does not have a type.
FATAL: Atom .R<I 4>.A<O4* 7> does not have a type.
FATAL: Atom .R<I 4>.A<C3* 8> does not have a type.
FATAL: Atom .R<I 4>.A<O3* 9> does not have a type.
FATAL: Atom .R<I 4>.A<C2* 10> does not have a type.
FATAL: Atom .R<I 4>.A<C1* 11> does not have a type.
FATAL: Atom .R<I 4>.A<N9 12> does not have a type.
FATAL: Atom .R<I 4>.A<C8 13> does not have a type.
FATAL: Atom .R<I 4>.A<N7 14> does not have a type.
FATAL: Atom .R<I 4>.A<C5 15> does not have a type.
FATAL: Atom .R<I 4>.A<C6 16> does not have a type.
FATAL: Atom .R<I 4>.A<O6 17> does not have a type.
FATAL: Atom .R<I 4>.A<N1 18> does not have a type.
FATAL: Atom .R<I 4>.A<C2 19> does not have a type.
FATAL: Atom .R<I 4>.A<N3 20> does not have a type.
FATAL: Atom .R<I 4>.A<C4 21> does not have a type.
FATAL: Atom .R<I 16>.A<P 1> does not have a type.
FATAL: Atom .R<I 16>.A<O1P 2> does not have a type.
FATAL: Atom .R<I 16>.A<O2P 3> does not have a type.
FATAL: Atom .R<I 16>.A<O5* 4> does not have a type.
FATAL: Atom .R<I 16>.A<C5* 5> does not have a type.
FATAL: Atom .R<I 16>.A<C4* 6> does not have a type.
FATAL: Atom .R<I 16>.A<O4* 7> does not have a type.
FATAL: Atom .R<I 16>.A<C3* 8> does not have a type.
FATAL: Atom .R<I 16>.A<O3* 9> does not have a type.
FATAL: Atom .R<I 16>.A<C2* 10> does not have a type.
FATAL: Atom .R<I 16>.A<C1* 11> does not have a type.
FATAL: Atom .R<I 16>.A<N9 12> does not have a type.
FATAL: Atom .R<I 16>.A<C8 13> does not have a type.
FATAL: Atom .R<I 16>.A<N7 14> does not have a type.
FATAL: Atom .R<I 16>.A<C5 15> does not have a type.
FATAL: Atom .R<I 16>.A<C6 16> does not have a type.
FATAL: Atom .R<I 16>.A<O6 17> does not have a type.
FATAL: Atom .R<I 16>.A<N1 18> does not have a type.
FATAL: Atom .R<I 16>.A<C2 19> does not have a type.
FATAL: Atom .R<I 16>.A<N3 20> does not have a type.
FATAL: Atom .R<I 16>.A<C4 21> does not have a type.
Warning: Close contact of 2.227075 angstroms between .R<I 4>.A<P 1> and
..R<I 4>.A<O1P 2>
Warning: Close contact of 2.112997 angstroms between .R<I 4>.A<O5* 4> and
..R<I 4>.A<C5* 5>
Warning: Close contact of 2.056286 angstroms between .R<I 4>.A<C4* 6> and
..R<I 4>.A<O4* 7>
Warning: Close contact of 2.130275 angstroms between .R<I 4>.A<O4* 7> and
..R<I 4>.A<C1* 11>
Warning: Close contact of 2.031530 angstroms between .R<I 4>.A<C3* 8> and
..R<I 4>.A<O3* 9>
Warning: Close contact of 2.128521 angstroms between .R<I 4>.A<C1* 11> and
..R<I 4>.A<N9 12>
Warning: Close contact of 1.884737 angstroms between .R<I 4>.A<N9 12> and
..R<I 4>.A<C8 13>
Warning: Close contact of 1.902573 angstroms between .R<I 4>.A<N9 12> and
..R<I 4>.A<C4 21>
Warning: Close contact of 1.702553 angstroms between .R<I 4>.A<C8 13> and
..R<I 4>.A<N7 14>
Warning: Close contact of 1.940131 angstroms between .R<I 4>.A<N7 14> and
..R<I 4>.A<C5 15>
Warning: Close contact of 2.003906 angstroms between .R<I 4>.A<C5 15> and
..R<I 4>.A<C6 16>
Warning: Close contact of 1.900210 angstroms between .R<I 4>.A<C5 15> and
..R<I 4>.A<C4 21>
Warning: Close contact of 1.757997 angstroms between .R<I 4>.A<C2 19> and
..R<I 4>.A<N3 20>
Warning: Close contact of 1.828728 angstroms between .R<I 4>.A<N3 20> and
..R<I 4>.A<C4 21>
Warning: Close contact of 1.906372 angstroms between .R<DT 7>.A<H2'1 30>
and .R<DT 8>.A<H73 20>
Warning: Close contact of 1.683294 angstroms between .R<DT 7>.A<H6 15> and
..R<WAT 80>.A<H2 2>
Warning: Close contact of 2.049009 angstroms between .R<DC5 13>.A<H4' 7>
and .R<WAT 85>.A<H2 2>
Warning: Close contact of 2.234678 angstroms between .R<I 16>.A<P 1> and
..R<I 16>.A<O1P 2>
Warning: Close contact of 2.205161 angstroms between .R<I 16>.A<P 1> and
..R<I 16>.A<O2P 3>
Warning: Close contact of 2.108776 angstroms between .R<I 16>.A<O5* 4> and
..R<I 16>.A<C5* 5>
Warning: Close contact of 2.025754 angstroms between .R<I 16>.A<C4* 6> and
..R<I 16>.A<O4* 7>
Warning: Close contact of 2.140657 angstroms between .R<I 16>.A<O4* 7> and
..R<I 16>.A<C1* 11>
Warning: Close contact of 2.067512 angstroms between .R<I 16>.A<C3* 8> and
..R<I 16>.A<O3* 9>
Warning: Close contact of 2.196929 angstroms between .R<I 16>.A<C2* 10>
and .R<I 16>.A<C1* 11>
Warning: Close contact of 2.161470 angstroms between .R<I 16>.A<C1* 11>
and .R<I 16>.A<N9 12>
Warning: Close contact of 1.887606 angstroms between .R<I 16>.A<N9 12> and
..R<I 16>.A<C8 13>
Warning: Close contact of 1.898921 angstroms between .R<I 16>.A<N9 12> and
..R<I 16>.A<C4 21>
Warning: Close contact of 1.688006 angstroms between .R<I 16>.A<C8 13> and
..R<I 16>.A<N7 14>
Warning: Close contact of 1.944459 angstroms between .R<I 16>.A<N7 14> and
..R<I 16>.A<C5 15>
Warning: Close contact of 1.996430 angstroms between .R<I 16>.A<C5 15> and
..R<I 16>.A<C6 16>
Warning: Close contact of 1.878150 angstroms between .R<I 16>.A<C5 15> and
..R<I 16>.A<C4 21>
Warning: Close contact of 1.772366 angstroms between .R<I 16>.A<C2 19> and
..R<I 16>.A<N3 20>
Warning: Close contact of 1.821729 angstroms between .R<I 16>.A<N3 20> and
..R<I 16>.A<C4 21>
Warning: Close contact of 1.817375 angstroms between .R<DT 19>.A<H2'2 31>
and .R<DT 20>.A<H5'1 6>
Warning: Close contact of 2.018619 angstroms between .R<WAT 25>.A<H2 2>
and .R<WAT 80>.A<H1 1>
Checking parameters for unit 'model'.
Checking for bond parameters.
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Checking for angle parameters.
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
There are missing parameters.
check: Errors: 42 Warnings: 36
Can somebody please suggest how do i make leap recognise inosine? Would i
also require a new parameter set for inosine?
Regards,
Arvind.
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Received on Tue Mar 23 2004 - 17:53:00 PST
