[gmx-users] Re: gmx-users Digest, Vol 101, Issue 52

[Justin Lemkul]

Please don't reply to the entire digest.

On 9/18/12 9:09 AM, Praveen Kumar Sappidi wrote:
> Dr Justin
> This is my Topolofy file for Ethanol
> [ moleculetype ]
> ; Name            nrexcl
> Protein             3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
> chargeB      massB
>       1          H      1   ETHH     EH      1      0.408      1.008   ; qtot 0.408
>       2         OA      1   ETHH     EO      1     -0.674    15.9994   ; qtot
> -0.266
>       3        CH2      1   ETHH    EC1      1      0.266     14.027   ; qtot 0
>       4        CH3      1   ETHH    EC2      2          0     15.035   ; qtot 0
>

The atom names are such that g_hbond does not recognize what atoms they are. 
g_hbond guesses donors and acceptors based on whether they are H, N, or O atoms 
and expects the first character of the atom name to be one of these.  Names 
starting with "E" will be unrecognized.  Rename the atoms and create a new .tpr 
file to run the analysis.

-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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