[gmx-users] pdb2gmx fails on CHARMM36 terminal group

[Davit Hakobyan]

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.