On Tue, Feb 14, 2012, Atila Petrosian wrote:
>
> I know for simulation with solvent, I should use following step:
>
> 1) $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03
> 2) dna = loadpdb "dna.pdb"
> 3) addions dna Na+ 0
> 4) solvatebox dna TIP3PBOX 8.0 iso
>
> If I want to do md simulation of dna without solvent, what command
> should I use instead of step 4
You should skip both steps 3 and 4, and just issue a "saveAmberParm" command.
Then turn on gb during the simulation. Note that this is certainly an
imperfect subsitute for explicit solvent, however.
...good luck....dac
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Received on Tue Feb 14 2012 - 05:00:02 PST
