[gmx-users] pdb2gmx fails on CHARMM36 terminal group

[Davit Hakobyan]

Thank you.

I have put the ZIP of the PDB file here: 
https://uni-muenster.sciebo.de/index.php/s/hO1OwfWMwwOy7xe
The encountered error with the ASP residue relates to the C-terminal 
patch of the ANAA molecule which pdb2gmx missed and treating it as an 
unpatched ASP would give, of course, a mismatch error.

Thanks a lot again for any suggestion.
Davit



On 3/13/2017 6:15 PM, Mark Abraham wrote:
> 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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