AMBER Archive (2007)

Subject: RE: AMBER: Attaching capping groups

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Apr 11 2007 - 22:49:36 CDT


Dear Neelanjana,
 
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
 
mol = sequence { ACE ALA NME }
saveamberparm mol prmtop inpcrd
 
will accomplish what you want to do.
 
Good luck...
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.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.

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Neelanjana Sengupta
Sent: Wednesday, April 11, 2007 18:29
To: amber_at_scripps.edu
Subject: AMBER: Attaching capping groups

Hi,

I want to create alanine dipeptide by including the capping groups ACE and
CTE (see below) to the N-terminus and C-terminus of alanine. Do I need to
modify the leaprc file for this?
I am using amber7. I could not identify suitable terminal groups in the
all_aminoct94.lib and all_aminont94.lib.
Some advice is greatly appreciated.

'ACE' is (C=O)-(CH3)
'CTE' is (CH3)-(NH)

Thanks,

-- 
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry 
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921
email: sengupta_at_uci.edu
**************************************** 

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu