[gmx-users] error with changing pdb file

[ksm tprk]

Hello,
While I am simulating my simulations, I encountered below error. I have pdb file which is:
HEADER    PROTEINTITLE     (5,5) Nanotube (1,1,80) replicationAUTHOR    TubeGen 3.3, J T Frey, University of DelawareEXPDTA    THEORETICAL MODELATOM      1  C   UNK     1       3.410   0.000 -98.494  1.00  0.00ATOM      2  C   UNK     1       3.113   1.390 -98.494  1.00  0.00ATOM      3  C   UNK     1       2.758   2.004 -97.263  1.00  0.00ATOM      4  C   UNK     1       1.702   2.954 -97.263  1.00  0.00ATOM      5  C   UNK     1       1.054   3.243 -98.494  1.00  0.00ATOM      6  C   UNK     1      -0.360   3.391 -98.494  1.00  0.00ATOM      7  C   UNK     1      -1.054   3.243 -97.263  1.00  0.00ATOM      8  C   UNK     1      -2.284   2.532 -97.263  1.00  0.00ATOM      9  C   UNK     1      -2.758   2.004 -98.494  1.00  0.00...
CONECT 1596 1595 1597CONECT 1597 1576 1596 1598CONECT 1598 1579 1597 1599CONECT 1599 1598 1600CONECT 1600 1581 1599MASTER        0    0    0    0    0    0    0    0 1600    0 1600    0END   

But by using text editor, I change an atom with another atom.And I created .top and .gro files respectively.( my sample is basically similar to Christopher Stiles' work, http://cs86.com/CNSE/SWNT.htm)

After I run my simulation, it gives the error:


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#checking input for internal consistency...calling cpp...processing topology...Generated 1282 of the 1485 non-bonded parameter combinationsWARNING 1 [file "cnt_500.top", line 72238]:  No default Angle types, using zeroesWARNING 2 [file "cnt_500.top", line 72238]:  No default Angle types for perturbed atoms, using normal valuesWARNING 3 [file "cnt_500.top", line 72239]:  No default Angle types, using zeroesWARNING 4 [file "cnt_500.top", line 72239]:  No default Angle types for perturbed atoms, using normal valuesWARNING 5 [file "cnt_500.top", line 72240]:  No default Angle types, using zeroesWARNING 6 [file "cnt_500.top", line 72240]:  No default Angle types for perturbed atoms, using normal valuesWARNING 7 [file "cnt_500.top", line 72241]:  No default Angle types, using zeroesWARNING 8 [file "cnt_500.top", line 72241]:  No default Angle types for perturbed atoms, using normal valuesWARNING 9 [file "cnt_500.top", line 72242]:  No default Angle types, using zeroesWARNING 10 [file "cnt_500.top", line 72242]:  No default Angle types for perturbed atoms, using normal valuesCleaning up temporary file gromppYFxvHw-------------------------------------------------------Program grompp_mpi, VERSION 3.3.1Source code file: fatal.c, line: 416
Fatal error:Too many warnings, grompp_mpi terminated-------------------------------------------------------

Without changing my pdb file, there was no error but after I can an atom with another, I got above error.Is there anyone who had same problem before? I will really appreciate if you can help me. 
Thank you,Kasim 		 	   		  
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