ksm tprk wrote:
Hi Justin,
I will try to be more clear. What I did, first I created a carbon
nanotube using Tubegen carbon nanotube generator. After that I changed
one carbon atom with another atom using text editor.
My ffgmx file is same as what http://cs86.com/CNSE/SWNT.htm has.
Next I created .top by applying ffgmx.n2t force field and .gro file
respectively. And I used grompp to run my simulation. And What I got the
error is:
OK, the problem is pretty straightforward now. You have a nitrogen atom within
a CNT, and there are no suitable angle parameters for such a system. The atom
type chosen is simply "N," which (from the ffgmx.atp file) corresponds to a
peptide nitrogen in an amide, which is not what is present in your system so
this assignment is incorrect. Perhaps "NR6" might be more appropriate?
-Justin
creating statusfile for 8 nodes...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
calling cpp...
processing topology...
Generated 1282 of the 1485 non-bonded parameter combinations
WARNING 1 [file "cnt80.top", line 11144]:
No default Angle types, using zeroes
WARNING 2 [file "cnt80.top", line 11144]:
No default Angle types for perturbed atoms, using normal values
WARNING 3 [file "cnt80.top", line 11145]:
No default Angle types, using zeroes
WARNING 4 [file "cnt80.top", line 11145]:
No default Angle types for perturbed atoms, using normal values
WARNING 5 [file "cnt80.top", line 11187]:
No default Angle types, using zeroes
WARNING 6 [file "cnt80.top", line 11187]:
No default Angle types for perturbed atoms, using normal values
WARNING 7 [file "cnt80.top", line 11189]:
No default Angle types, using zeroes
WARNING 8 [file "cnt80.top", line 11189]:
No default Angle types for perturbed atoms, using normal values
WARNING 9 [file "cnt80.top", line 11190]:
No default Angle types, using zeroes
WARNING 10 [file "cnt80.top", line 11190]:
No default Angle types for perturbed atoms, using normal values
Cleaning up temporary file grompp5QOA9q
-------------------------------------------------------
Program grompp_mpi, VERSION 3.3.1
Source code file: fatal.c, line: 416
The error atom is 25th atom. and the error lines specified in topology
file are( I underlined and made bold them):
.....
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 20 1
1 2 3 1
2 3 4 1
2 3 22 1
4 3 22 1
3 4 5 1
* 3 4 25 1*
* 5 4 25 1*
* * 4 5 6 1
5 6 7 1
6 7 8 1
6 7 26 1
8 7 26 1
7 8 9 1
7 8 29 1
9 8 29 1
8 9 10 1
9 10 11 1
10 11 12 1
10 11 30 1
12 11 30 1
11 12 13 1
11 12 33 1
13 12 33 1
12 13 14 1
13 14 15 1
14 15 16 1
14 15 34 1
16 15 34 1
15 16 17 1
15 16 37 1
17 16 37 1
16 17 18 1
17 18 19 1
18 19 20 1
18 19 38 1
20 19 38 1
1 20 19 1
1 20 21 1
19 20 21 1
20 21 22 1
20 21 40 1
22 21 40 1
3 22 21 1
3 22 23 1
21 22 23 1
22 23 24 1
22 23 42 1
24 23 42 1
* 23 24 25 1*
23 24 45 1
*25 24 45 1*
* 4 25 24 1*
4 25 26 1
24 25 26 1
7 26 25 1
.....
I attached topology and coordinate files too.
I am sorry that I gave not enough information.
Thank you,
Kasim
> I can't keep trying to help you if you don't provide relevant
information. If
> you want free help, you have to make it easy for those trying to help
you. This
> topology snippet is not at all what I asked to see. To be clear,
please post
> the following information:
>
> 1. The lines from the topology specified in the grompp error messages
(the line
> numbers are given in the error messages)
> 2. The coordinate file entries that correspond to the atoms on those
lines. It
> would be helpful to see the coordinate file that works, as well as
the one that
> was modified that no longer works.
>
> Going back to your very first post, the root of the problem is that
there are
> not bonded parameters in the ffgmx force field to describe whatever
changes you
> made. Since you have yet to actually demonstrate what these changes
were and
> how the affected the topology, there is no better help that anyone
can provide.
>
> -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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========================================
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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