AMBER Archive (2008)

Subject: Re: AMBER: drawing repeated units

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Tue Jun 03 2008 - 17:25:59 CDT

Hi Ross,
I have been trying to create the sequence correctly. I defined FPRT
(first part) REPU (repeated unit) and ENDU (end unit)

all three units have a tail and a head using set head set tail
functions. I also saved the structures in their own *.lib files similar
to the (Simulating a Solvated Protein that Contains Non-Standard
Residues (More Advanced Version))

in xleap i tried mymol = sequence { FPRT REPU REPU REPU ENDU } i got
FATAL ERROR
FATAL: in file [chiraliy.c], line 140
FATAL: Message: Atom named C12 from REPU did not match !

ABORTING.

question: in the files i set up does amber remove the hydrogen from C12
and create a connection? In other words my structures have a head and
tail atoms (carbon atoms) with 4 bonds, should they have 3 bonds
instead? or am i completely off interpreting this error.

Best,
Taufik

P.S. i am using AMBER 9 on IRIX64 6.5

Ross Walker wrote:
> 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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