[gmx-users] error with changing pdb file

[Justin A. Lemkul]

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

-- 
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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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