[gmx-users] pdb2gmx fails on CHARMM36 terminal group

[Davit Hakobyan]

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.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>