You also need a protein ff.
On Thu, Apr 26, 2012 at 10:17 AM, Lachele Foley (Lists)
<lf.list.gmail.com> wrote:
> 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
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Apr 26 2012 - 07:30:05 PDT
