hi
i started simulating protein in 8M urea conditions.
the problem is coming in defining urea box.
i did following commands in use (as given in manual for methanol)
source leaprc.ff99SB
loadAmberParams frcmod.urea
peptide = loadpdb file.pdb
solvateBox peptide 8MUREABOX 12.0 0.8
saveAmberParm peptide prmtop prmcrd
quit
here i used frcmod.urea for calculating Parameters for urea (or urea-water
mixtures)
error is that its not adding the solvent and error is:
Solvatebox <Solute> <Solvent> <Buffer> [aniso] [closeness] [iso]
can anyone help to solve the problem
thanx
monica
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Received on Wed Jun 23 2010 - 00:00:03 PDT
