hello guys:
thank you very much for kind advices. here is what I did:
setBox mol vdw
set mol box { 59.566 59.566 96.412 }
when I load it into VMD by command:
vmd apo.prmtop -rst7 apo.inpcrd
I get information:
Box Dimensions are 59.566002 59.566002 96.412003 90.000000
90.000000 90.000000
However, when I type command in vmd : pbc box
it said:
-error Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000).
Have you forgotten to set the pbc parameters?
I am just wondering why it doesn't display the pbc box?
thank you very much
Albert
On 05/09/2012 10:36 PM, Bill Ross wrote:
> usage: setBox<unit> vdw|centers [ clearance |<clearance_xyz_list> ]
>
> As I remember it, setBox takes the unit and, without reorienting
> it, uses either vdw boundaries or atom centers to draw a box with
> an optional clearance in all directions or an optional list of
> clearances in the x,y,z directions. If the box is already equilibrated,
> the vdw option would introduce voids at the edges which would take
> more equilibration than otherwise, but since the system needs to be
> warmed up anyway, this is probably not a factor.
>
> Bill
>
> Albert<mailmd2011.gmail.com> wrote:
>
>> Hello Jason:
>> thank you very much for your kind helps.
>> I generate the system from CHARMM GUI and it contains solvent, ions
>> and protein for a full MD system, then I import it into tleap to
>> generate Amber input file. I've obtained the periodic information such as:
>>
>> CRYST1 59.566 59.566 96.412 90.00 90.00 90.00 P 1 1
>>
>> I don't find detailed comments for this 'setBox' in the manual or online
>> tutorial expect helps from tleap:
>>
>> usage: setBox<unit> vdw|centers [ clearance |<clearance_xyz_list> ]
>>
>> do you have any idea how should I use this command correctly? Probably
>> like the following?
>>
>> setBox 0 0 0 59.566 59.566 96.412
>>
>>
>>
>>
>> On 05/09/2012 09:41 PM, Jason Swails wrote:
>>> You can use the "setBox" command in tleap to add periodic box information.
>>> If you add a solvent box, this should be done automatically.
>>>
>>> HTH,
>>> Jason
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Received on Thu May 10 2012 - 00:00:04 PDT
