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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