AMBER Archive (2009)

Subject: Re: [AMBER] (no subject)

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Mon Jun 08 2009 - 06:38:42 CDT

Hi Vishal,

        You can build a polymer using the "sequence" command in tleap. If you want to
create a system that has many polymers (eg. for a simulation using a periodic
boundary), you can use the "solvateDontClip" command in tleap. This is best
for isotactic polymers

        For atactic or syndiotactic polymers you will have to do something more
elaborate. For each polymer that has a unique sequence of tacticity, you will
have to create an entity within tleap using the sequence command - for
example:
poly1 = sequence {AAA AAA BBB AAA }
poly2 = sequence {AAA BBB BBB AAA }

Then use the "translate" command to place them in xyz space. Finally, once you
have them placed in xyz space, then use the "combine" command to get them all
together. This is doable, but time consuming.

Both ways (for isotactic and syndio- atactic polymers) create a very
artificial initial configuration, where the polymers are placed in a regular
order that resembles a crystal lattice.

Then you will have to figure out the best way to relax your system. There is
no easy solution in AMBER, that I am aware of, that will allow you to obtain
a random distribution of conformations and entanglement (if your polymer
length is long enough) starting from a sequence of resdues.

For branching, I would follow the example that is in the Amber9 manual for
carbohydrates.

Cheers,
Karl

On Monday 08 June 2009 13:14, Vishal Maingi wrote:
> dear sir,
> in amber is there any option of loop to be used in polymer building. can I
> use any loop command ,if there, to grow the polymer further using my own
> residues stored in abc.lib file another question is regarding the branched
> polymer building. is there any option to build the polymer by branching
> along with linear growth although linear growth can be done.
>
> thanks
>
> Vishal
> India
>
>
> From Chandigarh to Chennai - find friends all over India. Go to
> http://in.promos.yahoo.com/groups/citygroups/

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