AMBER Archive (2008)

Subject: Re: AMBER: drawing repeated units

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Tue Jun 03 2008 - 18:58:25 CDT

Thank you Ross,
It worked!
Where can i learn to create a simple leaprc file. is it in any of the
tutorials?

i can also type mymol = sequence { FPRT REPU ... 50 100 150 and 200
times.. ENDU } if writing a one -long- line script is too difficult.

Best,
Taufi

Ross Walker wrote:
> 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
>
>
> /\
> \/
> |\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 |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu