[gmx-users] pdb2gmx fails on CHARMM36 terminal group

[Davit Hakobyan]

Just a small note about cholesterol CHL1 in the merged.rtp file of 
november 2016 release for CHARMM36 force field.
The first four lines of CHL1 in merged.rtp:
        C3  CRL1    0.140  0
        O3   OHL   -0.660  1
       H3'   HOL    0.430  2
        H3  HGA1    0.090  3

While the sequence should be:
        C3  CRL1    0.140  0
        H3  HGA1    0.090  3
        O3   OHL   -0.660  1
       H3'   HOL    0.430  2

So that each hydrogen atom follow immediately the heavy atom. One could 
have this in mind for the next release?
Thanks again.

On 3/13/2017 6:41 PM, Davit Hakobyan wrote:
> Thank you very much!
>
> Indeed, it seems the problem was in the missing TER lines in 
> combination with -chainsep for individual chain separation.
>
> Thank you again for all your kind help.
> Davit
>
> On 3/13/2017 6:21 PM, Justin Lemkul wrote:
>>
>>
>> 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.
>>>>> -- 
>>>>> Gromacs Users mailing list
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>>
>