[gmx-users] Simulation in octanol as solvent

nur avneet nuravneet at yahoo.co.in
Thu Mar 15 10:37:08 CET 2007

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...
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