Hello everyone,
I am new to AMBER so let me quickly beg your pardon in case my challenge is
too simple.
I'm trying to build the prmtop and inpcrd from Xleap for DNA-CISPLATIN
complex (PDB ID : 2npw). Following some tutorials and using force field
parameters from previous work, I have been able edit the complex (which I
just called dna) to include the atom types PT for Platinum, NB1/NB2 for the
N7 guanine bound to Pt, N31/N32 for the Pt-bound ligand nitrogen, H3 for
the Proton bound to N31/N32. I then saved the changes in library (called
dna.lib).
Afterwords I typed the following commands in tleap
> source leaprc.DNA.OL15
> source leaprc.gaff
>loadoff dna.lib
> check dna
Checking 'dna'....
WARNING: The unperturbed charge of the unit: -22.000000 is not zero.
WARNING: The perturbed charge: -22.000000 is not zero.
Warning: Close contact of 1.451279 angstroms between .R<DG 7>.A<H21 24> and
.R<DC 18>.A<O2 24>
Checking parameters for unit 'dna'.
Checking for bond parameters.
Could not find bond parameter for: NB1 - CB
Could not find bond parameter for: NB1 - PT
No bond parameter for: NB - PT
Could not find bond parameter for: CK - NB1
Could not find bond parameter for: NB2 - CB
Could not find bond parameter for: NB2 - PT
No bond parameter for: NB - PT
Could not find bond parameter for: CK - NB2
Could not find bond parameter for: PT - N31
No bond parameter for: PT - N31
Could not find bond parameter for: PT - N32
No bond parameter for: PT - N32
Could not find bond parameter for: N31 - H3
No bond parameter for: N31 - H3
Could not find bond parameter for: N31 - H3
No bond parameter for: N31 - H3
Could not find bond parameter for: N31 - H3
No bond parameter for: N31 - H3
Could not find bond parameter for: N32 - H3
No bond parameter for: N32 - H3
Could not find bond parameter for: N32 - H3
No bond parameter for: N32 - H3
Could not find bond parameter for: N32 - H3
No bond parameter for: N32 - H3
Checking for angle parameters.
Could not find angle parameter: CB - NB1 - PT
Can't find angle parameter: CB - NB - PT
Could not find angle parameter: NB1 - CB - C
Could not find angle parameter: NB1 - CB - CB
Could not find angle parameter: NB1 - PT - NB2
Can't find angle parameter: NB - PT - NB
Could not find angle parameter: NB1 - PT - N31
Can't find angle parameter: NB - PT - N31
Could not find angle parameter: NB1 - PT - N32
Can't find angle parameter: NB - PT - N32
Could not find angle parameter: H5 - CK - NB1
Could not find angle parameter: CK - NB1 - CB
Could not find angle parameter: CK - NB1 - PT
Can't find angle parameter: CK - NB - PT
Could not find angle parameter: N* - CK - NB1
Could not find angle parameter: CB - NB2 - PT
Can't find angle parameter: CB - NB - PT
Could not find angle parameter: NB2 - CB - C
Could not find angle parameter: NB2 - CB - CB
Could not find angle parameter: NB2 - PT - N31
Can't find angle parameter: NB - PT - N31
Could not find angle parameter: NB2 - PT - N32
Can't find angle parameter: NB - PT - N32
Could not find angle parameter: H5 - CK - NB2
Could not find angle parameter: CK - NB2 - CB
Could not find angle parameter: CK - NB2 - PT
Can't find angle parameter: CK - NB - PT
Could not find angle parameter: N* - CK - NB2
Could not find angle parameter: PT - N31 - H3
Can't find angle parameter: PT - N31 - H3
Could not find angle parameter: PT - N31 - H3
Can't find angle parameter: PT - N31 - H3
Could not find angle parameter: PT - N31 - H3
Can't find angle parameter: PT - N31 - H3
Could not find angle parameter: PT - N32 - H3
Can't find angle parameter: PT - N32 - H3
Could not find angle parameter: PT - N32 - H3
Can't find angle parameter: PT - N32 - H3
Could not find angle parameter: PT - N32 - H3
Can't find angle parameter: PT - N32 - H3
Could not find angle parameter: N31 - PT - N32
Can't find angle parameter: N31 - PT - N32
Could not find angle parameter: H3 - N31 - H3
Can't find angle parameter: H3 - N31 - H3
Could not find angle parameter: H3 - N31 - H3
Can't find angle parameter: H3 - N31 - H3
Could not find angle parameter: H3 - N31 - H3
Can't find angle parameter: H3 - N31 - H3
Could not find angle parameter: H3 - N32 - H3
Can't find angle parameter: H3 - N32 - H3
Could not find angle parameter: H3 - N32 - H3
Can't find angle parameter: H3 - N32 - H3
Could not find angle parameter: H3 - N32 - H3
Can't find angle parameter: H3 - N32 - H3
There are missing parameters.
check: Warnings: 3
Unit is OK.
Afterwords , I typed this:
>loadamberparams dna.frcmod
>check dna
Checking 'dna'....
WARNING: The unperturbed charge of the unit: -22.000000 is not zero.
WARNING: The perturbed charge: -22.000000 is not zero.
Warning: Close contact of 1.451279 angstroms between .R<DG 7>.A<H21 24> and
.R<DC 18>.A<O2 24>
Checking parameters for unit 'dna'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 3
Unit is OK.
Lastly I typed
>saveamberparm dna prmtop inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -22.000000 is not zero.
WARNING: The perturbed charge: -22.000000 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
** No torsion terms for CB-CB-NB1-PT
** No torsion terms for C-CB-NB1-PT
** No torsion terms for CB-NB1-PT-NB2
** No torsion terms for CB-NB1-PT-N31
** No torsion terms for CB-NB1-PT-N32
** No torsion terms for NB1-PT-NB2-CB
** No torsion terms for NB1-PT-NB2-CK
** No torsion terms for NB1-PT-N31-H3
** No torsion terms for NB1-PT-N31-H3
** No torsion terms for NB1-PT-N31-H3
** No torsion terms for NB1-PT-N32-H3
** No torsion terms for NB1-PT-N32-H3
** No torsion terms for NB1-PT-N32-H3
** No torsion terms for H5-CK-NB1-CB
** No torsion terms for H5-CK-NB1-PT
** No torsion terms for CK-NB1-CB-C
** No torsion terms for CK-NB1-CB-CB
** No torsion terms for CK-NB1-PT-NB2
** No torsion terms for CK-NB1-PT-N31
** No torsion terms for CK-NB1-PT-N32
** No torsion terms for N*-CK-NB1-CB
** No torsion terms for N*-CK-NB1-PT
** No torsion terms for CB-CB-NB2-PT
** No torsion terms for CB-NB2-PT-N31
** No torsion terms for CB-NB2-PT-N32
** No torsion terms for NB2-PT-N31-H3
** No torsion terms for NB2-PT-N31-H3
** No torsion terms for NB2-PT-N31-H3
** No torsion terms for NB2-PT-N32-H3
** No torsion terms for NB2-PT-N32-H3
** No torsion terms for NB2-PT-N32-H3
** No torsion terms for H5-CK-NB2-CB
** No torsion terms for H5-CK-NB2-PT
** No torsion terms for CK-NB2-CB-C
** No torsion terms for CK-NB2-CB-CB
** No torsion terms for CK-NB2-PT-N31
** No torsion terms for CK-NB2-PT-N32
** No torsion terms for N*-CK-NB2-CB
** No torsion terms for N*-CK-NB2-PT
** No torsion terms for N31-PT-N32-H3
** No torsion terms for N31-PT-N32-H3
** No torsion terms for N31-PT-N32-H3
** No torsion terms for N32-PT-N31-H3
** No torsion terms for N32-PT-N31-H3
** No torsion terms for N32-PT-N31-H3
Building improper torsion parameters.
total 141 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
So I don't understand why I kept having this response since I specified
these torsion parameters in my dna.frcmod file. I have attached the frcmod
file so you can take a look. Please note that the values are just for the
sake of learning, they are not all accurate.
Thank you.
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Received on Wed Nov 08 2017 - 03:30:03 PST
