Re: [AMBER] parameters for Lys-sugar leap errors

From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Thu, 26 Apr 2012 11:41:01 +0200

Dear Amber users,

I prepared the library for my non standard sugar-lys molecule, the FF atom types were also set. However after running leap I am getting still errors about missing parameters ...

I attached the .off and pdb file...
Could someone help me with that?

/Urszula


> loadoff MGR.off
Loading library: ./MGR.off
Loading: MGR
> x = loadpdb MGR.pdb
Loading PDB file: ./MGR.pdb
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO.
(Residue 1: LYS, Nonterminal, was not found in name map.)
(Residue 2: TYR, Nonterminal, was not found in name map.)
(Residue 3: VAL, Nonterminal, was not found in name map.)
(Residue 4: LYS, Nonterminal, was not found in name map.)
(Residue 5: GLN, Nonterminal, was not found in name map.)
(Residue 6: ASN, Nonterminal, was not found in name map.)
(Residue 7: THR, Nonterminal, was not found in name map.)
(Residue 8: LEU, Nonterminal, was not found in name map.)
(Residue 9: MGR, Nonterminal, was not found in name map.)
(Residue 10: LEU, Nonterminal, was not found in name map.)
(Residue 11: ALA, Nonterminal, was not found in name map.)
Mapped residue THR, term: Terminal/last, seq. number: 12 to: CTHR.
Joining NPRO - LYS
Joining LYS - TYR
Joining TYR - VAL
Joining VAL - LYS
Joining LYS - GLN
Joining GLN - ASN
Joining ASN - THR
Joining THR - LEU
Joining LEU - MGR
Joining MGR - LEU
Joining LEU - ALA
Joining ALA - CTHR
  total atoms in file: 118
  Leap added 131 missing atoms according to residue templates:
       131 H / lone pairs
> check x
Checking 'x'....
WARNING: The unperturbed charge of the unit: 2.999800 is not zero.
Warning: Close contact of 1.389613 angstroms between .R<MGR 10>.A<H4 42> and .R<MGR 10>.A<H3 38>
Warning: Close contact of 0.496778 angstroms between .R<MGR 10>.A<H4 42> and .R<MGR 10>.A<C3 37>
Warning: Close contact of 0.693199 angstroms between .R<MGR 10>.A<H4 42> and .R<MGR 10>.A<H2 34>
Warning: Close contact of 1.386247 angstroms between .R<MGR 10>.A<HO3 40> and .R<CTHR 13>.A<HG1 12>
Warning: Close contact of 1.253929 angstroms between .R<MGR 10>.A<H3 38> and .R<MGR 10>.A<H2 34>
Warning: Close contact of 1.395009 angstroms between .R<MGR 10>.A<H3 38> and .R<CTHR 13>.A<OG1 11>
Warning: Close contact of 0.466877 angstroms between .R<MGR 10>.A<C3 37> and .R<MGR 10>.A<H2 34>
Warning: Close contact of 1.462857 angstroms between .R<MGR 10>.A<H1 27> and .R<LEU 11>.A<O 19>
Warning: Close contact of 1.327867 angstroms between .R<MGR 10>.A<C 5> and .R<LEU 11>.A<N 1>
Checking parameters for unit 'x'.
Checking for bond parameters.
Could not find bond parameter for: CG - H1
Could not find bond parameter for: CG - OH
Could not find bond parameter for: CG - H1
Could not find bond parameter for: CG - OH
Could not find bond parameter for: CG - CG
Could not find bond parameter for: CG - H1
Could not find bond parameter for: CG - OH
Could not find bond parameter for: CG - CG
Could not find bond parameter for: CG - H1
Could not find bond parameter for: CG - H1
Could not find bond parameter for: CG - OH
Could not find bond parameter for: CG - H
Could not find bond parameter for: CG - CG
Could not find bond parameter for: CG - CG
Could not find bond parameter for: OS - CG
Could not find bond parameter for: CG - H1
Could not find bond parameter for: CG - OS
Could not find bond parameter for: CG - CG
Could not find bond parameter for: O - CG
Could not find bond parameter for: C - H
Could not find bond parameter for: C - H
Could not find bond parameter for: C - H
Could not find bond parameter for: C - H
Could not find bond parameter for: C - H
Could not find bond parameter for: C - H
Could not find bond parameter for: C - H
Could not find bond parameter for: O - N
Could not find bond parameter for: C - H
Could not find bond parameter for: N - H2
Checking for angle parameters.
Could not find angle parameter: C - N - H2
Could not find angle parameter: C - N - C
Could not find angle parameter: H1 - CG - OH
Could not find angle parameter: CG - OH - HO
Could not find angle parameter: OH - CG - CG
Could not find angle parameter: H1 - CG - OH
Could not find angle parameter: H1 - CG - CG
Could not find angle parameter: CG - OH - HO
Could not find angle parameter: CG - CG - H1
Could not find angle parameter: CG - CG - OH
Could not find angle parameter: OH - CG - CG
Could not find angle parameter: H1 - CG - OH
Could not find angle parameter: H1 - CG - CG
Could not find angle parameter: CG - OH - HO
Could not find angle parameter: CG - CG - H1
Could not find angle parameter: CG - CG - OH
Could not find angle parameter: CG - CG - CG
Could not find angle parameter: H1 - CG - OH
Could not find angle parameter: H1 - CG - H1
Could not find angle parameter: H1 - CG - OH
Could not find angle parameter: CG - CG - CG
Could not find angle parameter: CG - OH - HO
Could not find angle parameter: H - CG - CG
Could not find angle parameter: H - CG - CG
Could not find angle parameter: CG - CG - H1
Could not find angle parameter: CG - CG - H1
Could not find angle parameter: CG - CG - OH
Could not find angle parameter: CG - CG - H1
Could not find angle parameter: CG - CG - OH
Could not find angle parameter: CG - CG - CG
Could not find angle parameter: OS - CG - CG
Could not find angle parameter: OS - CG - H
Could not find angle parameter: OS - CG - CG
Could not find angle parameter: OS - CG - CG
Could not find angle parameter: H1 - CG - OS
Could not find angle parameter: H1 - CG - CG
Could not find angle parameter: CG - OS - CG
Could not find angle parameter: CG - CG - CG
Could not find angle parameter: CG - CG - H1
Could not find angle parameter: CG - CG - OH
Could not find angle parameter: O - CG - H1
Could not find angle parameter: O - CG - OS
Could not find angle parameter: O - CG - CG
Could not find angle parameter: H - C - N
Could not find angle parameter: H - C - H
Could not find angle parameter: H - C - N
Could not find angle parameter: H - C - C
Could not find angle parameter: H - C - O
Could not find angle parameter: C - C - H
Could not find angle parameter: C - C - H
Could not find angle parameter: C - C - N
Could not find angle parameter: C - O - CG
Could not find angle parameter: H - C - C
Could not find angle parameter: H - C - H
Could not find angle parameter: H - C - C
Could not find angle parameter: C - C - H
Could not find angle parameter: C - C - C
Could not find angle parameter: H - C - C
Could not find angle parameter: H - C - H
Could not find angle parameter: H - C - C
Could not find angle parameter: C - C - H
Could not find angle parameter: C - C - H
Could not find angle parameter: C - C - C
Could not find angle parameter: O - N - H
Could not find angle parameter: O - N - CT
Could not find angle parameter: C - C - C
Could not find angle parameter: C - O - N
Could not find angle parameter: H - C - C
Could not find angle parameter: H - C - C
Could not find angle parameter: C - C - H
Could not find angle parameter: C - C - H
Could not find angle parameter: C - C - C
Could not find angle parameter: H2 - N - C
Could not find angle parameter: N - C - H
Could not find angle parameter: N - C - C
Could not find angle parameter: N - C - C
There are missing parameters.
check: Warnings: 10
Unit is OK.

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Thu Apr 26 2012 - 03:00:04 PDT
Custom Search