You need to load GLYCAM parameters to use those atom types.
On Thu, Apr 26, 2012 at 5:41 AM, Urszula Uciechowska
<urszula.uciechowska.chem.umu.se> wrote:
> 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.
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Apr 26 2012 - 07:30:04 PDT
