[gmx-users] Error regarding pdb2gmx of modified residue

[Amir Zeb]

Alright Mark,

pdb2gmx does not give me output file in complete, it crashes before the
generation of top and gro files for the protein, while generating the above
mentioned fatal error.

~Amir

On Mon, Jan 1, 2018 at 11:21 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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