[gmx-users] pdb2gmx fails on CHARMM36 terminal group

[Mark Abraham]

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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