[gmx-users] Incorrect number of atomtypes for dihedral

[Justin Lemkul]

On 7/20/12 2:26 PM, Debashis Sahu wrote:
> Dear user,
>
>                  I have used this RB dihedral for thiourea in
> ff-bonded.itp file, which is the error line mentioning below:
>
> dih_THI_H_N_C_S                             23.10000  -2.10000
> -21.00000   0.00000   0.00000   0.00000
>
> dih_THI_H_N_C_N                             20.50160   0.00000
> -20.50160   0.00000   0.00000   0.00000
>

If these are your exact lines, they are incorrectly formatted.  They should be 
declared as #define statements.  See existing examples in ffbonded.itp.

-Justin

> The thiourea which I used in .rtp file given below:
>
> [ THI ] ; thiourea added in by DEBASHIS SAHU
>   [ atoms ]
>      C	   opls_247          0.287	      1	
>      S	   opls_038         -0.523            2	
>     N1	   opls_249          0.076            3	
>    H11   opls_250          0.021	      4
>    H12	   opls_250          0.021	      5	
>     N2	   opls_249          0.076            6	
>    H21	   opls_250          0.021	      7	
>    H22	   opls_250          0.021	      8	
>   [ bonds ]
>      C	  N1
>      C	  N2
>      C	   S
>     N1    H11
>     N1    H12
>     N2    H21
>     N2    H22
>   [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>     S     C    N1   H12     dih_THI_H_N_C_S
>     S     C    N2   H22     dih_THI_H_N_C_S
>     N2    C    N1   H11    dih_THI_H_N_C_N
>     N1    C    N2   H21    dih_THI_H_N_C_N
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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