[gmx-users] Simulation in octanol as solvent

Erik Marklund erikm at xray.bmc.uu.se
Thu Mar 15 12:12:13 CET 2007

15 mar 2007 kl. 10.37 skrev nur avneet:

> Dear All
> I have added octanolas solvent...but now my problem is that if i  
> take the itp file as available on the gromacs site (which is in  
> ffoplsaa) there are too many warnings related to bond types and if  
> i get an itp generated through prodrg then it excludes the  
> aliphatic hydrogens, while my gro file has all hydrogens and hence  
> thereafter the coordinates donot match....
> What should i do??
> Should i remove all hydrogens from the octanol gro file...and if  
> yes is there any command to do so...as its very tedious to remove  
> all hydrogens from 512 molecules...



> Regrds
> nur
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

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