[AMBER] Failed to generate parameters

From: Sadaf Rani <sadafrani6.gmail.com>
Date: Sat, 11 May 2019 16:48:41 +0100

I am trying to follow the amber tutorial TUTORIAL B5 Simulating the Green
Fluorescent Protein. When I run tleap I get following error message:-

The file contained 6 atoms not in residue templates
Checking Unit.
WARNING: There is a bond of 4.982997 angstroms between:
------- .R<CMET 87>.A<SD 11> and .R<CMET 87>.A<CE 12>
WARNING: There is a bond of 3.615864 angstroms between:
------- .R<CMET 87>.A<CG 8> and .R<CMET 87>.A<HG2 9>
WARNING: There is a bond of 3.428284 angstroms between:
------- .R<CMET 87>.A<CG 8> and .R<CMET 87>.A<HG3 10>
WARNING: There is a bond of 6.282434 angstroms between:
------- .R<CMET 219>.A<SD 11> and .R<CMET 219>.A<CE 12>
WARNING: There is a bond of 3.254820 angstroms between:
------- .R<CMET 219>.A<CG 8> and .R<CMET 219>.A<HG2 9>
WARNING: There is a bond of 3.171454 angstroms between:
------- .R<CMET 219>.A<CB 5> and .R<CMET 219>.A<HB2 6>
WARNING: There is a bond of 3.659759 angstroms between:
------- .R<CMET 219>.A<CB 5> and .R<CMET 219>.A<HB3 7>
WARNING: There is a bond of 4.853690 angstroms between:
------- .R<CMET 219>.A<N 1> and .R<CMET 219>.A<H 2>
WARNING: The unperturbed charge of the unit: -7.000003 is not zero.
FATAL: Atom .R<CMET 75>.A<SE 19> does not have a type.
FATAL: Atom .R<NLYS 76>.A<H 25> does not have a type.
FATAL: Atom .R<ME 86>.A<SD 1> does not have a type.
FATAL: Atom .R<NALA 153>.A<H 13> does not have a type.
FATAL: Atom .R<ME 218>.A<SD 1> does not have a type.
FATAL: Atom .R<NVAL 220>.A<H 19> does not have a type.
Failed to generate parameters
Parameter file was not saved.

Please anyone can tell me where I am doing wrong? I am new to amber and I
tried different tutorials but get stucked at this point of parameter
generation. I have attached leap.log file.


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Received on Sat May 11 2019 - 09:00:02 PDT
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