On Thu, Jan 25, 2018, Amen Shamim wrote:
>
> 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
> 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>
Of course, you should check your input structure to figure out what is going
on with the above very odd distances.
> 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
This seems pretty clear: atom types CI (etc) are not defined in your input
parameters. I'm not sure where all_prot_nucleic10.lib came from, but
it clearly seems based on nucleic10.lib, which is the current nucleic
acid library. But you are loading oldff/leaprc.ff03, which points to
earlier RNA libraries that don't have atom types like CI, C4, etc.
Note that loading oldff/leaprc.ff03 is quite dangerous! You are getting
truly old RNA parameters, that will almost certainly give results you don't
want. Remember that the files in the "oldff" directory are really only there
for the purposes of checking or reproducing old simulations. The RNA
parameters in leaprc.ff03 are now 25 years old.
I'm guessing that you should instead source leaprc.RNA.OL3.
....dac
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Received on Thu Jan 25 2018 - 07:00:02 PST
