[gmx-users] Terminal dangling bond error despite pdb2gmx recognising specbond.dat for a cyclic peptide

[Sahil Lall]

Dear community, 

I want to use the OPLS-AA ff to understand the dynamics of a cyclic
peptide with terminal-peptide-bonded Cystines that are also disulphide
linked (i.e CxxxxxxC). To cyclise the N- and C- termini, I used a
special bond in a specbond.dat file placed in my working directory. 

2
CYS N 1 CYS C 1 0.14 CYS CYS
CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 

and after the pdb2gmx command I get the following response 

Identified residue CYS2 as a starting terminus.
Identified residue CYS7 as a ending terminus.
2 out of 2 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                    CYS2    CYS2    CYS2    CYS7    CYS7
                      N1      C3     SG6     N45     C47
    CYS2      C3   0.244
    CYS2     SG6   0.312   0.419
    CYS7     N45   0.335   0.510   0.486
    CYS7     C47   0.136   0.373   0.322   0.239
    CYS7    SG50   0.387   0.482   0.205   0.420   0.365
Linking CYS-2 N-1 and CYS-7 C-47...
Linking CYS-2 SG-6 and CYS-7 SG-50... 

However, the problem arises with the -ter flag in the pdb2gmx command 

pdb2gmx -f in.pdb -o out.gro -ter -ignh 

The output is fine and links the terminal Cystines and putting a
disulphide bond between them as shown above. But doesn't seem to be
happy with the -ter command. 

Select start terminus type for CYS-2
0: NH3+
1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
residue)
2: NH2
3: None
3
Start terminus CYS-2: None
Select end terminus type for CYS-7
0: COO-
1: ZWITTERION_COO- (only use with zwitterions containing exactly one
residue)
2: COOH
3: None
3
End terminus CYS-7: None 

-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.7
Source code file:
/home/ncbs/Downloads/gromacs-4.6.7/src/kernel/pdb2top.c, line: 1109 

Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
------------------------------------------------------- 

I cannot understand what is going wrong. The command only works if I
choose NH2 as my N-terminus, however that in-principle violates the
valence of the amide N and neutrality of the system. 

Thanks, 

Sahil