[gmx-users] CNT

[Justin A. Lemkul]

trevor brown wrote:
> Dear Justin,
> Regarding our previous discussion under "CNT" topic, you want to know 
> exactly what I did to define C-C interaction. I have summarized it below.
>  
> 1. I copied oplsaa.ff folder in my working directory
> 2. I added following lines to atomname2type.n2t
> C    opls_995    0      12.011  2    C  0.142  C 0.142
> C    opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
> C    opls_997    0      12.011  4    C  0.142  C 0.142  C 0.142 C 0.142
> C    opls_998    0      12.011  5    C  0.142  C 0.142  C 0.142 C 0.142 
> C 0.142
> 3. I added those to atomtypes.atp
>  opls_995   12.01100  ; 
>  opls_996   12.01100  ; 
>  opls_997   12.01100  ; 
>  opls_998   12.01100  ;  
>  
> 4. I added those to ffbonded.itp
> [ bondtypes ]
>   C     C    1   0.14210   478900
>  [ angletypes ]
>   C   C    C  1 120.000 562.2
>  [ dihedraltypes ]
> 5. I constructed .top file for CNT with the following, then I converted 
> it into .itp by vi editor
> g_x2top -f cnt.gro -o cnt.top -nopairs -nexcl 5
> 6. By pdb2gmx, I obtained .top for peptide then I converted it into .itp  
> 7. I combined CNT and peptide's pdbs in pymol and saved.
> 8. I wrote a .top file given below,
> ;
> ; File 'topol.top' was generated
> ; By user: onbekend (0)
> ; On host: onbekend
> ; At date: Mon Jan 10 02:51:19 2011
> ;
> ; This is a standalone topology file
> ;
> ; It was generated using program:
> ; pdb2gmx - VERSION 4.5.3
> ;
> ; Command line was:
> ; pdb2gmx -ignh -f vpgvg10.pdb
> ;
> ; Force field was read from the standard Gromacs share directory.
> ;
> ; Include forcefield parameters
> #include "forcefield.itp"
> 

Be careful with this - if you move this topology between directories, it will 
call any forcefield.itp file that may be in the working directory.  What did you 
remove the "oplsaa.ff" prefix?

> ; Include topology for CNT
> #include "cnt.itp"
> ; Include topology for UW1
> #include "uw1.itp"
> ; Include water topology
> #include "spc.itp"
> [ system ]
> ; Name
> Protein and CNT in water
> [ molecules ]
> ; Compound        #mols
> Protein             1
> CNT                 1
> SOL                 4019          
> 9. When I make grompp for minimization it givea me the following error
> WARNING 1 [file ffbonded.itp, line 2703]:
>   Overriding Bond parameters.
>   old: 0.151 292880 0.151 292880
>   new: C     C    1   0.14210   478900
> 
> ERROR 1 [file ffbonded.itp, line 2707]:
>   Not enough parameters
> Generated 334153 of the 334153 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 334153 of the 334153 1-4 parameter combinations
> -------------------------------------------------------
> Program grompp, VERSION 4.5.3
> Source code file: toppush.c, line: 1166
> Fatal error:
> Atomtype opls_996 not found
>  
> That is all what I exactly did. Is anything wrong or missing?
>  

You never defined nonbonded parameters for your new atom type.  You've declared 
that it exists in the .atp file, but then you didn't add that atom type in 
ffnonbonded.itp.

-Justin

> best wishes
> trevor
>   
> 
>  
> 

-- 
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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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