[gmx-users] H-atoms in .hdb file

[Justin A. Lemkul]

On 6/26/12 11:36 AM, Shima Arasteh wrote:
> I tried again as below:
> 1. defined FOR in .rtp file
> 2. defined FOR in aminoacids.dat file.
> 3. chose NH2 as N-Terminal
>
> and then got this topology for FOR and VAL:
> ; residue   0 FOR rtp FOR  q  0.0
>       1        CH1      0    FOR      C      1       0.38     13.019   ; qtot 0.38
>       2          O      0    FOR      O      1      -0.38    15.9994   ; qtot 0
> ; residue   1 VAL rtp VAL  q  0.0
>       3         NL      1    VAL      N      2      -0.83    14.0067   ; qtot -0.83
>       4          H      1    VAL     H1      2      0.415      1.008   ; qtot -0.415
>       5          H      1    VAL     H2      2      0.415      1.008   ; qtot 0
>       6        CH1      1    VAL     CA      3          0     13.019   ; qtot 0
>       7        CH1      1    VAL     CB      4          0     13.019   ; qtot 0
>       8        CH3      1    VAL    CG1      5          0     15.035   ; qtot 0
>       9        CH3      1    VAL    CG2      6          0     15.035   ; qtot 0
>      10          C      1    VAL      C      7       0.38     12.011   ; qtot 0.38
>      11          O      1    VAL      O      7      -0.38    15.9994   ; qtot 0
>
> I guess the topology is correct. Isn't it?
>
>

No, it isn't.  An NH2 terminal says the N-terminus of VAL is a neutral amine. 
You should choose "None" for the terminus.  The formyl group occupies the 
N-terminus as would another amino acid in a peptide bond, but there is no 
special protonation of FOR.

-Justin

-- 
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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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