[gmx-users] problem still there for ACE

[Albert]

Hello:

I capped the protein with residues ACE and NMA at N-ter and C-ter 
respectively. Here is the coordinate:

ATOM      1  CH3 ACE X  38       9.945  21.608  90.016  1.00 
0.00           C
ATOM      4 HH31HACE X  38      10.267  21.376  91.056  1.00 
0.00           H
ATOM      5 HH32HACE X  38       9.614  22.669  89.956  1.00 
0.00           H
ATOM      6 HH33HACE X  38       9.095  20.947  89.733  1.00 
0.00           H
ATOM      2  C   ACE X  38      11.113  21.380  89.058  1.00 
0.00           C
ATOM      3  O   ACE X  38      12.196  20.997  89.497  1.00 
0.00           O
ATOM      4  N   GLY X  39      10.957  21.602  87.705  1.00 
0.00           N
ATOM      5  CA  GLY X  39      12.077  21.382  86.795  1.00 
0.00           C
ATOM      6  C   GLY X  39      11.787  21.661  85.315  1.00 
0.00           C
ATOM      7  O   GLY X  39      12.527  21.182  84.455  1.00 
0.00           O

....

ATOM   2309  N   LYS X 335      38.981  11.135  41.177  1.00 
0.00           N
ATOM   2310  CA  LYS X 335      40.402  10.845  41.347  1.00 
0.00           C
ATOM   2311  C   LYS X 335      40.881  11.426  42.687  1.00 
0.00           C
ATOM   2312  O   LYS X 335      41.551  12.456  42.677  1.00 
0.00           O
ATOM   2313  CB  LYS X 335      41.191  11.366  40.117  1.00 
0.00           C
ATOM   2314  CG  LYS X 335      40.902  10.605  38.817  1.00 
0.00           C
ATOM   2315  CD  LYS X 335      41.781  11.075  37.647  1.00 
0.00           C
ATOM   2316  CE  LYS X 335      41.492  10.315  36.347  1.00 
0.00           C
ATOM   2317  NZ  LYS X 335      42.382  10.755  35.267  1.00 
0.00           N1+
ATOM   4782  N   NMA X 335      40.573  10.815  43.885  1.00 
0.00           N
ATOM   4784  H   NMA X 335      40.023   9.969  43.894  1.00 
0.00           H
ATOM   4783 CH3  NMA X 335      41.042  11.390  45.138  1.00 
0.00           C
ATOM   4785 HH31 NMA X 335      41.625  12.311  44.913  1.00 
0.00           H
ATOM   4786 HH32 NMA X 335      40.172  11.644  45.784  1.00 
0.00           H
ATOM   4787 HH33 NMA X 335      41.688  10.657  45.670  1.00 
0.00           H
END



When I try to run command:

pdb2gmx -f p.pdb -o gmx.pdb  -ter

Select start terminus type for ACE-38
  0: NH3+
  1: NH2
  2: 5TER
  3: None
3
Start terminus ACE-38: None
Select end terminus type for LYS-335
  0: COO-
  1: COOH
  2: CT2
  3: 3TER
  4: None
4
End terminus LYS-335: 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.


When I run command:

pdb2gmx -f p.pdb -o gmx.pdb

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


I noticed this thread:
https://www.mail-archive.com/gmx-users@gromacs.org/msg49517.html

and Justine said there is a N atom on ACE instead of the first atom of 
the next residue. However, as shown in my coordinate, there is NO atom N 
in ACE at all. And I cannot figure out what's the problem....

thanks a lot

Albert