[gmx-users] additional peptide bond: cyclic peptides

[andrea spitaleri]

Hi Giacomo,
you need to put a distance cut-off of 0.14 since the amidic bond C-N is around 0.133 nm
check the syntax of specbond.dat

Regards

Andrea

Giacomo Bastianelli wrote:
> Dear Gromacs user,
> 
> I tried to modify the specbond.dat file to introduce the
> an additional peptide-bond to make a peptide cyclic.
> 
> The pdbgmx2 reads correctly the specbond.dat file
> 
> and is able to make a matrix of distances.
> 
> However, it does not form any "linking" between the
> 
> two specified atoms.
> 
> see below the specbond.dat file and the pdbgmx2 log:
> -------------------------------------------------------------
> 
> 6
> CYS    SG    1    CYS    SG    1    0.2    CYS2    CYS2
> CYS    SG    1    HEME    FE    2    0.25    CYS2    HEME
> CYS    SG    1    HEME    CAB    1    0.2    CYS2    HEME
> CYS    SG    1    HEME    CAC    1    0.2    CYS2    HEME
> HIS    NE2    1    HEME    FE    1    0.2    HIS1    HEME
> CYS2    NL    1    VAL    C    1    0.2    CYS2    VAL
> ----------------------------------------------
> Opening library file 
> /home/Bis/gbastian/my_gromacs_data/share/gromacs/top/specbond.dat
> 6 out of 6 lines of specbond.dat converted succesfully
> Special Atom Distance matrix:
>                    CYS1    CYS5    VAL6   CYS10   CYS15   CYS17   VAL21
>                     SG4    SG30     C38    SG58    SG90   SG103    C138
>    CYS5    SG30   0.917
>    VAL6     C38   1.396   0.585
>   CYS10    SG58   0.655   0.422   0.857
>   CYS15    SG90   0.202   0.961   1.432   0.625
>   CYS17   SG103   1.039   0.204   0.625   0.487   1.056
>   VAL21    C138   0.685   0.388   0.847   0.531   0.802   0.569
>   CYS22   SG143   0.588   0.430   0.827   0.203   0.606   0.568   0.419
>   VAL29    C196   0.394   1.193   1.626   1.004   0.555   1.345   0.869
>                   CYS22
>                   SG143
>   VAL29    C196   0.886
> Linking CYS-1 SG-4 and CYS-15 SG-90...
> Linking CYS-5 SG-30 and CYS-17 SG-103...
> Linking CYS-10 SG-58 and CYS-22 SG-143...
> N-terminus: NH3+
> C-terminus: COO-
> Now there are 29 residues with 247 atoms
> Making bonds...
> ------------------------------------------
> 
> ...no bonds between my N-TERM and C-TERM
> 
> 
> Thanks in advance for your help,
> 
> Giacomo Bastianelli
> 
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-- 
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------

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