[gmx-users] error with changing pdb file
Justin A. Lemkul
jalemkul at vt.edu
Fri Dec 18 19:30:17 CET 2009
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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