[gmx-users] pdb2gmx fails on CHARMM36 terminal group

[Mark Abraham]

Hi,

Using -ter to specify where molecules end won't help if there are not any
TER records, but I can't tell what's in your file :-)

Mark

On Mon, Mar 13, 2017 at 6:12 PM Davit Hakobyan <dhako_01 at uni-muenster.de>
wrote:

> Thank you for the suggestion.
>
> I have tried to use the "-ter" flagbut this does not helpsince the
> problem is not because pdb2gmx cannot recognize the C-terminal patch,
> but that it misses the termianals of the intermediate proteins.The
> protein sequence in my system is like:
>
> ANAA,ANAC,P11A,P11C
>
> So even when I use the "-ter" flag the program asks to specify the
> N-termianl patch for ANAA and C-terminal patch for P11C. But all the
> four molecules are independent chains and each of them have both
> N-terminal (NH3+) and C-terminal (COO-). But pdb2gmx seems to treat them
> as a single long chain?
>
> Thanks again for any help.
> Davit
>
>
> On 3/13/2017 5:54 PM, Mark Abraham wrote:
> > Hi,
> >
> > pdb2gmx has options that configure its behaviour to let you choose
> whether
> > PDB TER records and/or changes of chain ID should separate molecules,
> etc.
> > You could explore those, and/or perhaps add such TER records to make your
> > intent clearer to the tool. (But with incomplete information, I can't be
> > sure that will help...)
> >
> > Mark
> >
> > On Mon, Mar 13, 2017 at 5:48 PM Davit Hakobyan <dhako_01 at uni-muenster.de
> >
> > wrote:
> >
> >> Dear All,
> >>
> >> I have a very big system with 4 proteins and membrane system. The
> >> relevant topology part is as follows:
> >>
> >> [ molecules ]
> >> ; Compound    #mols
> >> ANAA                 1
> >> ANAC                 1
> >> P11A                 1
> >> P11C                 1
> >> CHL1               190
> >> POPC               380
> >> DOPC               190
> >> POPI24              80
> >> POPS               160
> >> TIP3            179172
> >> SOD                770
> >> CLA                351
> >> CAL                 30
> >>
> >> The first four molecules are the proteins. Each of these molecules has
> >> CTER patch applied in CHARMM using charmm36 force field.
> >>
> >> During the convertion with pdb2gmx I get an error. Below are shown some
> >> relevant parts of the output:
> >>
> >> *Processing chain 1 (675703 atoms, 110937 residues)**
> >> **Identified residue MET1 as a starting terminus.**
> >> **Warning: Residue CHL11 in chain has different type (Other) from
> >> starting residue MET1 (Protein).**
> >> **Warning: Residue CHL12 in chain has different type (Other) from
> >> starting residue MET1 (Protein).**
> >> **Warning: Residue CHL13 in chain has different type (Other) from
> >> starting residue MET1 (Protein).**
> >> **Warning: Residue CHL14 in chain has different type (Other) from
> >> starting residue MET1 (Protein).**
> >> **Warning: Residue CHL15 in chain has different type (Other) from
> >> starting residue MET1 (Protein).**
> >> **More than 5 unidentified residues at end of chain - disabling further
> >> warnings.**
> >> **Identified residue LYS96 as a ending terminus.*
> >>
> >> Although there are warnings, however, the problem seems to be in another
> >> place. The next portion is the following:
> >>
> >> *Start terminus MET-1: NH3+**
> >> **End terminus LYS-96: COO-**
> >> **Opening force field file
> >>
> >>
> /home/d/dhako_01/bin/gromacs/share/gromacs/top/charmm36-nov2016.ff/merged.arn**
> >> *
> >>   From the above one can see that the program only detected the CTER of
> >> the P11C molecule (it is 96 residues large) and missed the CTERS of
> >> ANAA, ANAC and P11A. And now comes the actual error:
> >>
> >> *Program gmx_5.0.4_mpi, VERSION 5.0.4**
> >> **Source code file:
> >> /home/d/dhako_01/src/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c,
> >> line: 732**
> >> **
> >> **Fatal error:**
> >> **Atom OT1 in residue ASP 339 was not found in rtp entry ASP with 12
> >> atoms**
> >> **while sorting atoms.**
> >> *
> >> I guess the above error indicates that the pdb2gmx could not detect the
> >> CTER portion of ANAA/ANAC (their last residue is ASP) so the error
> appears.
> >>
> >> Could someone suggest a resolution?
> >>
> >> Thanks a lot in advance.
> >> --
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