Dear Dr. Case,
I modified the pdb file from VMD output, and it worked. Thank you.
Guoxiong
On Aug 30, 2010, at 4:31 PM, David A. Case wrote:
> On Mon, Aug 30, 2010, Guoxiong Su wrote:
>>
>> I am trying to solvate my molecule in a water spherocylinder in Leap. After
>> that I can run MD simulation about the system using Amber. I can solvate it
>> using VMD and some Tcl scripts. However, I don't know how to do it in LEaP.
>
> You can't do this easily in LEaP, so it's good you know how to do it in VMD.
> Have VMD output a pdb file, and use the loadPdb command in LEaP. Be aware,
> however, that you will have a molecules in the pdb, surrounded by vacuum.
>
> ...hope this helps....dac
>
>
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Received on Tue Aug 31 2010 - 07:30:05 PDT
