[gmx-users] pdb2gmx fails on CHARMM36 terminal group

[Justin Lemkul]

On 3/13/17 1:12 PM, Davit Hakobyan 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?
>

You need to use TER between chains or assign them different chain identifiers in 
the PDB file, otherwise pdb2gmx assumes they're continuous.  See -chainsep option.

-Justin

> 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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>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================