[gmx-users] Simulation in octanol as solvent

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 14 08:51:25 CET 2007

nur avneet wrote:
> Dear All
> I want to study a peptoid sequence in octanol as solvent
> Please guide me how to proceed.
> I got the octanol eqilibrated box topology files from GROMACS site, 
> (gromacs users contributors section)..but am not able to add my peptoid 
> sequence to it...moreover the octanol box model that i got is by the 
> ffoplsaa ...while my peptoid is from ffG43a1...
> I gave the editconf and then the genbox comand...but then it shows zero 
> solvent molecules that are added.
> can anyone guide me...hw to proceed

remove the hydrogens from octanl and update your topology. you can also 
make a topology at the prodrg web server. read chapter 5 of the manual.
> regards
> nur
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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