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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
--
========================================
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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