Dear Ross,
Thanks. This worked, producing the correct atoms. The coordinates of the
methyl hydrogens are, however, quite odd (see attached pdf for picture), but
it should work out during minimization. I just wanted to ask if this is
normal.... I am using amber7.
I did not use any initial coordinates for this case. I will soon be
simulating some artificial peptides which are capped at both ends by organic
groups, for which I have coordinates (as pdb files). Will I need to modify
the leaprc file? I would be very grateful if you could point out the steps
required to do this.
Regards,
Neelanjana
On 4/11/07, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> 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.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.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Neelanjana Sengupta
> *Sent:* Wednesday, April 11, 2007 18:29
> *To:* amber.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.uci.edu
> ****************************************
>
>
--
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921
email: sengupta.uci.edu
****************************************
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Received on Sun Apr 15 2007 - 06:07:32 PDT
