[gmx-users] CNT

[Justin A. Lemkul]

trevor brown wrote:
> Dear friends,
> I have the following topology for system including CNT+peptide+water
> When I grompp for minimization, I got the following error. How can I 
> solve it?
>  
> best wishes
> trevor
>  
> WARNING 1 [file ffbonded.itp, line 2703]:
>   Overriding Bond parameters.
>   old: 0.151 292880 0.151 292880
>   new: C  C 1   0.14210    478900
> 

You have a duplicate bondtype entry.  Seems like you've got explicit C-C bonds 
in one topology, and those parameters are replacing the default ones in 
ffbonded.itp.  Is that what you intend?

> ERROR 1 [file ffbonded.itp, line 2709]:
>   Not enough parameters
> 

In the ffbonded.itp provided in the Gromacs distribution, line 2709 is blank. 
What have you added here?

> -------------------------------------------------------
> Program grompp, VERSION 4.5.3
> Source code file: topio.c, line: 675
> Fatal error:
> Syntax error - File forcefield.itp, line 20
> Last line read:
> '1  3  yes  0.5 0.5'
> Found a second defaults directive.
>  

Something in your topology has gotten badly mangled.  You can only ever have one 
[defaults] directive that defines certain aspects of the force field.

http://www.gromacs.org/Documentation/Errors#Found_a_second_defaults_directive_file

>  
>  
> TOPOLOGY
> ; Include forcefield parameters
> #include "oplsaa.ff/forcefield.itp"
> 
> ; Include topology for CNT
> #include "cnt.itp"
> ; Include topology for UW1
> #include "uw1.itp"
> ; Include water topology
> #include "oplsaa.ff/spc.itp"
> [ system ]
> ; Name
> Protein and CNT in water
> [ molecules ]
> ; Compound        #mols
> Protein             1
> CNT                 1
> SOL                 4019
> 

In principle, this should work, if you've properly constructed the #included 
.itp files, but I suspect something is wrong with one or more of them.  Do any 
of them re-#include "oplsaa.ff/forcefield.itp" (the peptide topology perhaps)?

-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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