[gmx-users] pdb2gmx error with addition of terminal group

[anu chandra]

Dear Gromacs users,

I am trying to use pdb2gmx tool to generate topology for my membrane
protein system with chamrm36 force field. I have downloaded Gromacs
compatible Chamrmm36ff from
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the
N-terminal acetyl (ACE) and  C-terminal N-methyl amide (NMA) group attached
to the respective terminals. As shown below, I have named the residue/atom
names according to the one present in 'merged.rtp' in the charmm36ff file.

*******************************************************************************
ATOM      1  CH3 ACE     1      37.718  66.293  67.509  1.00  0.00      PROA
ATOM      2 HH31 ACE     1      36.850  66.906  67.178  1.00  0.00      PROA
ATOM      3 HH32 ACE     1      37.393  65.240  67.617  1.00  0.00      PROA
ATOM      4 HH33 ACE     1      38.522  66.381  66.751  1.00  0.00      PROA
ATOM      5  C   ACE     1      38.195  66.802  68.805  1.00  0.00      PROA
ATOM      6  O   ACE     1      37.657  67.757  69.352  1.00  0.00      PROA
ATOM      7  N   VAL     1      39.245  66.166  69.366  1.00  0.00      PROA
ATOM      8  HN  VAL     1      39.698  65.409  68.911  1.00  0.00      PROA
ATOM      9  CA  VAL     1      39.818  66.600  70.628  1.00  0.00      PROA
ATOM     10  HA  VAL     1      39.044  66.557  71.385  1.00  0.00      PROA
------------------------------------
------------------------------------
ATOM   2599  HG1 SER   165      47.684  67.280  81.712  1.00  0.00      PROA
ATOM   2600  C   SER   165      46.288  64.682  84.443  1.00  0.02      PROA
ATOM   2601  O   SER   165      46.621  64.090  85.417  1.00  0.04      PROA
ATOM   2602  N   NMA   166      45.020  64.893  84.635  1.00  0.03      PROA
ATOM   2603  HN  NMA   166      44.986  65.779  85.049  1.00  0.00      PROA
ATOM   2604  CH3 NMA   166      44.322  63.814  85.342  1.00  0.04      PROA
ATOM   2605 HH31 NMA   166      44.694  62.798  85.066  1.00  0.04      PROA
ATOM   2606 HH32 NMA   166      43.284  63.888  85.004  1.00  0.04      PROA
ATOM   2607 HH33 NMA   166      44.382  63.845  86.467  1.00  0.06      PROA
***********************************************************************************

But, when running ' gmx pdb2gmx -f  input.pdb -ter' and opting 'none' for
the terminal, the pogram terminate with following error

***********************************************************************************
Back Off! I just backed up topol.top to ./#topol.top#
Processing chain 1 (2607 atoms, 167 residues)
Identified residue ACE1 as a starting terminus.
Warning: Residue NMA166 in chain has different type (Other) from starting
residue ACE1 (Protein).
Identified residue SER165 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                   CYS64   CYS72   CYS95  MET100  CYS101
                  SG1007  SG1123  SG1473  SD1554  SG1568
   CYS72  SG1123   0.857
   CYS95  SG1473   2.147   1.806
  MET100  SD1554   2.390   1.830   0.806
  CYS101  SG1568   1.896   1.488   0.334   0.773
  MET143  SD2232   1.844   1.750   1.858   2.389   1.687
Select start terminus type for ACE-1
 0: NH3+
 1: NH2
 2: 5TER
 3: None
3
Start terminus ACE-1: None
Select end terminus type for SER-165
 0: COO-
 1: COOH
 2: CT2
 3: 3TER
 4: None
4
End terminus SER-165: None

-------------------------------------------------------
Program gmx, VERSION 5.0.4
Source code file:
/usr/local/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091

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
-------------------------------------------------------
**************************************************************************************

Can anybody help me to figure out what is wrong with my input pdb file?

Many thanks in advance

Anu