ksm tprk wrote:
Hello,
While I am simulating my simulations, I encountered below error.
I have pdb file which is:
HEADER PROTEIN
TITLE (5,5) Nanotube (1,1,80) replication
AUTHOR TubeGen 3.3, J T Frey, University of Delaware
EXPDTA THEORETICAL MODEL
ATOM 1 C UNK 1 3.410 0.000 -98.494 1.00 0.00
ATOM 2 C UNK 1 3.113 1.390 -98.494 1.00 0.00
ATOM 3 C UNK 1 2.758 2.004 -97.263 1.00 0.00
ATOM 4 C UNK 1 1.702 2.954 -97.263 1.00 0.00
ATOM 5 C UNK 1 1.054 3.243 -98.494 1.00 0.00
ATOM 6 C UNK 1 -0.360 3.391 -98.494 1.00 0.00
ATOM 7 C UNK 1 -1.054 3.243 -97.263 1.00 0.00
ATOM 8 C UNK 1 -2.284 2.532 -97.263 1.00 0.00
ATOM 9 C UNK 1 -2.758 2.004 -98.494 1.00 0.00
...
CONECT 1596 1595 1597
CONECT 1597 1576 1596 1598
CONECT 1598 1579 1597 1599
CONECT 1599 1598 1600
CONECT 1600 1581 1599
MASTER 0 0 0 0 0 0 0 0 1600 0 1600 0
END
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 combinations
WARNING 1 [file "cnt_500.top", line 72238]:
No default Angle types, using zeroes
WARNING 2 [file "cnt_500.top", line 72238]:
No default Angle types for perturbed atoms, using normal values
WARNING 3 [file "cnt_500.top", line 72239]:
No default Angle types, using zeroes
WARNING 4 [file "cnt_500.top", line 72239]:
No default Angle types for perturbed atoms, using normal values
WARNING 5 [file "cnt_500.top", line 72240]:
No default Angle types, using zeroes
WARNING 6 [file "cnt_500.top", line 72240]:
No default Angle types for perturbed atoms, using normal values
WARNING 7 [file "cnt_500.top", line 72241]:
No default Angle types, using zeroes
WARNING 8 [file "cnt_500.top", line 72241]:
No default Angle types for perturbed atoms, using normal values
WARNING 9 [file "cnt_500.top", line 72242]:
No default Angle types, using zeroes
WARNING 10 [file "cnt_500.top", line 72242]:
No default Angle types for perturbed atoms, using normal values
Cleaning up temporary file gromppYFxvHw
-------------------------------------------------------
Program grompp_mpi, VERSION 3.3.1
Source 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.
If you have altered the atom numbers or types without re-generating the
topology, then the angles in the topology will no longer make sense.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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