[gmx-users] additional peptide bond: cyclic peptides

[Giacomo Bastianelli]

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