AMBER Archive (2008)

Subject: RE: AMBER: drawing repeated units

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jun 03 2008 - 16:50:23 CDT

Hi Taufik,

> 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.

If I understand you correctly then yes your individual units should not have
the hydrogens there. E.g. consider if your individual units were simply
ethane that you would be joining together to make a linear alkane. I think
by your description your current unit would be:

   H H
H--C---C--H
   H H

Whereas it should look (for REPU):

   H H
   C---C
   H H

For FPRT it should be:

   H H
H--C---C
   H H

Etc.

Try that and see if it works.

All the best
Ross

/\
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|\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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