VMD-L Mailing List

From: Knut Jørgen Bjuland (knutjorgen_at_gmail.com)
Date: Sun Apr 18 2010 - 00:54:27 CDT

The problem is that vmd does not display the 3d strcuture in a right
manner. When I keep the chain information when I am making a pqr by
using pdb2pqr. If I chose not to include the chain vmd does display the
protein in folded state, but when chain information is prsent vmd
display the protein as unfoldes protein. I used 2OB0 as test case since
it is polypetid with chain A,B and C.

Den 17.04.2010 17:06, skrev Olaf Lenz:
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> On 04/17/2010 03:40 PM, bharat gupta wrote:
>
>> I kept my protein for simulation for 3ns duration but after 2ns
>> simulation it has started coming out of the simulation box and the
>> same thing happened with a friend of mine twice when he simulated his
>> protein for 3ns . In gromacs we can tackle the same problem by setting
>> the protein location to the centre of the box .. Can you tell me how
>> can I do this in using pbc tools in VMD.
>>
> There is no way to fix the protein to the center with help of the pbc
> tools. The pbc tools can only change which periodic box the atoms are in.
> However, you can implement a function that shifts all atoms so that the
> protein is always in the center in Tcl easily. Just have a look at the
> different Tcl functions that VMD provides (in the UG:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/)
> atomsel moveby (http://www.ks.uiuc.edu/Research/vmd/current/ug/node118.html)
> measure center (http://www.ks.uiuc.edu/Research/vmd/current/ug/node133.html)
>
> So, try something like (not tested, just from my mind):
>
> # replace PROTEIN-SEL with the selection expression for the protein
> set proteinsel [atomselect top "PROTEIN-SEL"]
> # compute the offset (center of the protein)
> set offset [vecinvert [measure center $proteinsel]}
>
> # select all atoms
> set allsel [atomselect top "all"]
> # move all atoms by the given offset
> $allsel moveby $center
>
> I would guess you'll have to adapt this until it works.
>
> Olaf
> - --
> A: Because it messes up the order in which people normally read text.
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> A: Top-posting.
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