Hi,
when it happens in my case, I erase the hidrogens that were reported as
"does not have a type" of the protein. When I do leap again, everything goes
right and leap adds the correct hydrogens.
_________________________________________________________________
De: "Carlos Simmerling" <carlos.simmerling.gmail.com>
Enviada: 2021/02/15 18:25:00
Para: amber.ambermd.org
Assunto: Re: [AMBER] tLeap, Fatal: Atom does not have a type
have you tried using pdb4amber to process your pdb file before loading it
into leap? that might help. if not you'll want to tell us more about
exactly how you obtained the pdb file.
On Mon, Feb 15, 2021 at 4:17 PM Alysia Mandato <alysiamandato.gmail.com>
wrote:
> Hello,
>
> After these steps:
>
> source leaprc.protein.ff14SB
> source leaprc.DNA.bsc1
> source leaprc.water.tip3p
> mol=loadpdb 4wlw_AB_NTA.pdb
>
> I get output in tleap which says that it "Created a new atom named: O01
> within residue ..." This is the same for P01, O02, O03, H01, H02, and H03.
> This is the only reason why I added those atom types. I am not sure why
> those atoms are added when I load in the PDB file.
>
> I am not sure how to add these properly in the lib file. I found these
> atoms in my structure on PyMol, and they are part of a phosphate backbone
> of my DNA strand. Maybe they should be different atom types? I'm having
> trouble determining what to do.
>
> Should I add these atom types somehow to the lib file, or is there a way
to
> rename the strange atom types to the typical phosphate backbone atoms (P,
> OP1, OP2)?
>
> On Fri, Feb 12, 2021 at 5:42 PM Maria Nagan <maria.c.nagan.gmail.com>
> wrote:
>
> > Alysia,
> >
> > Kenneth is right - you have weird atoms. What are O01, O02 and O03
> > representing?
> >
> > Do you have an extra protonated phosphate? That might be your problem.
> You
> > need your DNA residues to match the lib file you gave it (parmBSC1.lib).
> So
> > you need parameters for a residue with an extra phosphate.
> >
> > I’m not sure why you add PO1. What is that? Is it an O5’ or O3’?
> >
> > Remember that the only atom types allowed are the ones you define with
> > your leaprc files (found in $AMBERHOME/dat/leap/lib/parmBSC1.lib
> according
> > to your leaprc.DNA.bsc1).
> >
> > You shouldn’t have to add atom types P, OP1, OP2. These are standard in
> > parmBSC1.lib.
> >
> > Maria
> >
> > > On Feb 12, 2021, at 2:08 PM, Alysia Mandato <alysiamandato.gmail.com>
> > wrote:
> > >
> > > Hello all,
> > >
> > > I am solvating a protein-DNA system with a few modifications. I know
> > these
> > > modification steps work, but I am running into a fatal error when I
> check
> > > my pdb. I'm having a lot of trouble solving this fatal error in my
> tleap
> > > script. When I "check mol", I have fatal errors saying that I have
> atoms
> > > that do not have a type. I tried using the addAtomTypes command, and I
> am
> > > not sure I am doing it properly. Any guidance would be greatly
> > appreciated.
> > > These are the steps I am using:
> > >
> > > source leaprc.protein.ff14SB
> > > source leaprc.DNA.bsc1
> > > source leaprc.water.tip3p
> > > addAtomTypes {{ "P" "P" "sp3" }{ "OP1" "O" "sp2" }{ "OP2" "O" "sp2" }{
> > "PO1
> > > "P" "sp3" }{ "O01" "O" "sp2" }{ "O02" "O" "sp2" }{ "O03" "O" "sp2" }{
> > "HO1"
> > > "H" "sp3" }{ "HO2" "H" "sp3" }}
> > > loadamberprep HIC.prepi
> > > loadamberprep NTA.prepi
> > > loadamberparams HIC.frcmod2
> > > loadamberparams NTA.frcmod2
> > > mol=loadpdb 4wlw_AB_NTA.pdb
> > > bond mol.60.CA mol.333.C13 S
> > > bond mol.64.CA mol.333.C12 S
> > > bond mol.196.CA mol.334.C13 S
> > > bond mol.200.CA mol.334.C12 S
> > > solvateoct mol TIP3PBOX 15.0
> > > addions mol Cl- 228
> > > addions mol Na+ 228
> > > savepdb mol 4wlw_nta_solv_bonds.pdb
> > > check mol
> > > saveamberparm mol 4wlw_nta.prmtop 4wlw_nta.prmcrd
> > > quit
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> >
> >
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Received on Tue Feb 16 2021 - 04:00:02 PST
