[AMBER] Protonated cytosine and adenine: Parameter file was not saved

From: Amen Shamim <amenshamim.gmail.com>
Date: Thu, 25 Jan 2018 22:15:28 +0900

Dear Amber group,

I want to generate the protonated N3 of base cytosine (CP) and N1 of base
adenine (AP). When i loaded pdb it added missing heavy atom O2' and no
parameter file saved after adding ion and water box. I am using Amber16.
Here is my steps that i followed

>source oldff/leaprc.ff03
>loadoff all_prot_nucleic10.lib
>loadAmberParams frcmod.protonated_nucleic
>dna1=loadpdb motif.pdb
Loading PDB file: ./motif.pdb
  Added missing heavy atom: .R<CP 4>.A<O2' 29>
  Added missing heavy atom: .R<AP 13>.A<O2' 31>
  total atoms in file: 256
  Leap added 114 missing atoms according to residue templates:
       2 Heavy
       112 H / lone pairs
> addions dna1 Na+ 0
10 Na+ ions required to neutralize.
Adding 10 counter ions to "dna1" using 1A grid
Used default radius 1.50 for 5 atoms
Grid extends from solute vdw + 4.15 to 10.25
Resolution: 1.00 Angstrom.
grid build: 0 sec
 (no solvent present)
Calculating grid charges
charges: 0 sec
Placed Na+ in dna1 at (31.90, 68.25, -6.72).
Placed Na+ in dna1 at (23.90, 66.25, 4.28).
Placed Na+ in dna1 at (44.90, 56.25, -9.72).
Placed Na+ in dna1 at (31.90, 67.25, 12.28).
Placed Na+ in dna1 at (41.90, 66.25, -11.72).
Placed Na+ in dna1 at (29.90, 47.25, -6.72).
Placed Na+ in dna1 at (42.90, 73.25, 3.28).
Placed Na+ in dna1 at (23.90, 56.25, 6.28).
Placed Na+ in dna1 at (20.90, 66.25, -6.72).
Placed Na+ in dna1 at (40.90, 49.25, 0.28).

Done adding ions.
> solvatebox dna1 TIP3PBOX 10
 (using default radius 1.500000 for C5')
 (using default radius 1.500000 for C6)
 (using default radius 1.500000 for C5)
 (using default radius 1.500000 for C5')
 (using default radius 1.500000 for C8)
  Solute vdw bounding box: 27.736 29.736 28.195
  Total bounding box for atom centers: 47.736 49.736 48.195
  Solvent unit box: 18.774 18.774 18.774
 (using default radius 1.500000 for C5')
 (using default radius 1.500000 for C6)
 (using default radius 1.500000 for C5)
 (using default radius 1.500000 for C5')
 (using default radius 1.500000 for C8)
  Total vdw box size: 50.985 52.874 50.629 angstroms.
  Volume: 136486.948 A^3
  Mass > 61331.244 amu, Density > 0.746 g/cc
      (type - hence mass - of one or more atoms could not be found)
  Added 3197 residues.
> saveamberparm dna1 motif.prmtop motif.inpcrd
Checking Unit.
WARNING: There is a bond of 6.592593 angstroms between:
------- .R<DC 2>.A<C3' 25> and .R<DC 2>.A<H3' 26>
WARNING: There is a bond of 6.140893 angstroms between:
------- .R<DC 3>.A<C3' 25> and .R<DC 3>.A<H3' 26>
WARNING: There is a bond of 5.742315 angstroms between:
------- .R<CP 4>.A<H3' 26> and .R<CP 4>.A<C3' 25>
WARNING: There is a bond of 8.164783 angstroms between:
------- .R<DA 11>.A<C5' 5> and .R<DA 11>.A<H5'1 6>
WARNING: There is a bond of 7.927619 angstroms between:
------- .R<DA 12>.A<C5' 5> and .R<DA 12>.A<H5'1 6>
WARNING: There is a bond of 7.738285 angstroms between:
------- .R<AP 13>.A<H5' 6> and .R<AP 13>.A<C5' 5>

 -- ignoring the warnings.

Building topology.
Building atom parameters.
For atom: .R<CP 4>.A<C5' 5> Could not find vdW (or other) parameters for
type: CI
For atom: .R<CP 4>.A<C6 14> Could not find vdW (or other) parameters for
type: C4
For atom: .R<CP 4>.A<C5 16> Could not find vdW (or other) parameters for
type: C4
For atom: .R<AP 13>.A<C5' 5> Could not find vdW (or other) parameters for
type: CI
For atom: .R<AP 13>.A<C8 14> Could not find vdW (or other) parameters for
type: C5
Parameter file was not saved.
>

leap.log and my pdb file is attached with this email. Kindly, let me know
how i can resolve this problem.
Thanks

Best regards,
Amen


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Received on Thu Jan 25 2018 - 05:30:03 PST
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