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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 15 2021 - 13:30:02 PST
