AMBER Archive (2008)

Subject: RE: AMBER: drawing repeated units

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri May 09 2008 - 11:03:28 CDT

Hi Taufik,

> i was wondering if there is an automatic or an easy way to draw a
> oligomer in AMBER9. i have a an easy CH2-C(CH)(COC2OH5) unit. I would
> like to draw an oligomer that consist of 50, 100, 150 of these units. Is
> this possible?

Probably the easiest way to do this is to build a single unit in leap. Call
it residue foo or whatever and assign it head and tail atoms (equivalent to
the C and N in amino acids). Then you can assign it atoms type and charges (
you may have to build termini versions as well to deal with the capping -
i.e. protonated end points. You could call these Nfoo and CFoo.

Then once you have your units built you can have leap string them together
for you.

E.g. mymol = sequence { Nfoo foo foo foo Cfoo } etc.

To build very long ones you could write a shell script that creates a simple
leaprc script for you that you can then read back into xleap or tleap.

Of course this will give you straight chains which you may not want so if
you want to build some kind of bundle this may be harder and you'll probably
need some kind of input coordinates. Or build a more complex foo unit that
contains several units including the turns so that when leap applies the
z-matrix for each block you end up with a bundled structure.

Good luck,
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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