[gmx-users] Error regarding pdb2gmx of modified residue

[Mark Abraham]

Hi,

Just as Justin said there, I suspect you missed step 5 of
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

pdb2gmx should also have told you things about how many chains, etc. it
found. What was the full output?

Mark

On Tue, Jan 2, 2018 at 6:52 AM Amir Zeb <zebamir85 at gmail.com> wrote:

> Thanks Mark,
>
> Actually, the pdb file which I'm trying to execute for topology generation,
> has one residue (TYR15) is modified to phosphorylated tyrosine. Once I'm
> directing to command prompt for selection of termini, N-terminus is fine
> where it is needed for GLN-2, but the app asking C-terminus for THR-14
> which lies before TYR-15 (in this case TP2-15 which is explained in
> aforementioned email). I will attach the snap right here to let you clear
> the query.
>
> Select start terminus type for GLN-2
>  0: NH3+
>  1: NH2
>  2: 5TER
>  3: None
> 0
> Start terminus GLN-2: NH3+
> Select end terminus type for THR-14
>  0: COO-
>  1: COOH
>  2: CT2
>  3: 3TER
>  4: None
> 0
> End terminus THR-14: COO-
> Opening force field file ./charmm36-jul2017.ff/merged.arn
>
> So, I don't why am I getting this comment? The C-terminal residue of my pdb
> file is SER-287. Please let me know if possible why C-terminus is needed
> for THR-14 of the pdb file? If you kindly need more information, I will go
> through.
>
> Also, some has faced the similar issue here:
>
>
> https://www.researchgate.net/post/How_can_I_prevent_GROMACS_50_with_CHARMM36_from_wrongly_identifying_the_residue_preceding_a_phosphorylated_amino_acid_as_a_C-terminal
>
>
> But I couldn't follow, how to resolve it?
>
> Thanks!
>
> ~Amir
>
> On Mon, Jan 1, 2018 at 9:58 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > I would rename those atoms exactly as the .tdb file in your force field
> > expects. And if that doesn't work, try deleting them and having pdb2gmx
> > rebuild them.
> >
> > Mark
> >
> > On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb <zebamir85 at gmail.com> wrote:
> >
> > > Hi gmx users,
> > >
> > > Wishing you all a very happy new year 2k18.
> > >
> > > I have modified a particular Tyr residue to phosphorylated Tyr and
> > renamed
> > > as TP2 per forcefield recognizable name. I have used:
> > > gmx pdb2gmx -f xxx.pdb -o xxx.gro -ignh -ter (as full command)
> > > C36m ff
> > > Gromacs v5.0.6
> > > NH3+ as N-terminus
> > > COO- as C-terminus
> > > TIP3P water model
> > >
> > > I am getting error:
> > >
> > > Fatal error:
> > > Atom OXT in residue SER 287 was not found in rtp entry SER with 11
> atoms
> > > while sorting atoms.
> > >
> > > The C-terminus of my pdb file is pasted right here:
> > > ATOM   4538  OC1 SER A 287
> > > ATOM   4539  OC2 SER A 287
> > > TER      4540           SER A 287
> > > END
> > >
> > > I am aware of that SER 287 is C-terminus residue but by which name
> > should i
> > > replace the terminal oxygen to cope with this error?
> > >
> > > Looking forward for your kind suggestions.
> > >
> > > Thanks in advance!
> > >
> > > ~Amir
> > > --
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