In terminal:
This is the command i have used to load forcefield parameters
"$AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB"
and for loading ion parameters, i have used this
"loadamberparamsfrcmod.ionsjc_tip3p"
In xleap window:
I have loaded the DNA molecule into xleap using
"dna1 = loadpdb "myname.pdb"
saved the topology and coordinate file using
"saveamberparm dna1 polyAT_vac.prmtop polyAT_vac.inpcrd"
added Na+ ions using the command
"addions dna1 Na+ 0"
again tried to save topology and coordinate file for neutralised system
"saveamberparm dna1 polyAT_cio.prmtop polyAT_cio.inpcrd"
after this i got error message parameter file was not saved.
--
With kind regards,
G. Sreemol
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Received on Thu Mar 03 2016 - 21:30:05 PST
