[gmx-users] No default U-B types in CHARMM36 FF

[Albert]

Hello Mark:

thanks a lot for kind comments. I tried following selections:

Select start terminus type for ACE-35
  0: NH3+
  1: NH2
  2: 5TER
  3: None
3
Start terminus ACE-35: None
Select end terminus type for GLY-338
  0: COO-
  1: COOH
  2: CT2
  3: 3TER
  4: None
4
End terminus GLY-338: None

-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.5
Source code file: /home/albert/gromacs-4.6.5/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
-------------------------------------------------------


It still failed. I don't understand, there is a NMA in the C-term, why 
the second dialog ask the GLY-338 instead of NMA residue?

thanks a lot

ALbert




On 04/13/2014 03:55 PM, Mark Abraham wrote:
> And did you choose "none" for the termini generation? Otherwise when
> pdb2gmx tries to combine the default tdb option with your residue, it'll
> fail because... drum roll... there's no nitrogen!
>
> Mark