[gmx-users] asking for N and C termini for DNA and giving error

[Sucharita Dey]

Hello,

My protein is pr-DNA complex, it is identifying DNA terminus and searching for N and C in tdb  file giving error. When I select -ter and specify none as termini , it still gives error saying

"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. " Please help.

Error without -ter option:

Processing chain 1 'B' (434 atoms, 21 residues) 
Identified residue DADE1 as a starting terminus. 
Identified residue DTHY21 as a ending terminus. 
8 out of 8 lines of specbond.dat converted successfully 
Start terminus DADE-1: NH3+ 
End terminus DTHY-21: COO- 

------------------------------------------------------- 
Program pdb2gmx, VERSION 4.6.3 
Source code file: /home/sucharita/sucharita/softwares/gromacs_all/gromacs-4.6.3/src/kernel/pdb2top.c, line: 1148 

Fatal error: 
atom N not found in buiding block 1DADE while combining tdb and rtp 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors 


with -ter option selecting none

Processing chain 1 'B' (434 atoms, 21 residues) 
Identified residue DADE1 as a starting terminus. 
Identified residue DTHY21 as a ending terminus. 
8 out of 8 lines of specbond.dat converted successfully 
Select start terminus type for DADE-1 
 0: NH3+ 
 1: NH2 
 2: None 
2 
Start terminus DADE-1: None 
Select end terminus type for DTHY-21 
 0: COO- 
 1: COOH 
 2: None 
2 
End terminus DTHY-21: None 

------------------------------------------------------- 
Program pdb2gmx, VERSION 4.6.3 
Source code file: /home/sucharita/sucharita/softwares/gromacs_all/gromacs-4.6.3/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 
------------------------------------------------------- 

Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, National University of Singapore. 14, Medical Drive,  #12-01, Singapore 117599. Tel: (65) 90355220, email: csisd at nus.edu.sg