Re: AMBER: Querry

From: Carlos Simmerling <>
Date: Tue, 26 Aug 2008 10:09:25 -0400

tell us more about what you are doing. are you reading a pdb file? if
so, make sure there is no TER line and it will automatically connect
the chains if they are in the right order.
for the BOND command problem, without knowing exactly what leap said
it is hard to help. there should be no problem with the C-N bond, but
maybe there is something else going on. perhaps it already made them
terminal residues and added the extra H and O? try removing the TER
and see if it helps, if not then show us the relevant lines from the
leap.log file (not the whole file).

On Tue, Aug 26, 2008 at 7:50 AM, dipti lele <> wrote:
> Hello all,
> I have two seperate peptides (to be precise one protein and another
> peptide) i have to join them together at the C terminal end. How can I do
> it? How can i do it using leap? i have given the BOND command but leap is
> not able to find the bond parameters for C- N bond.
> What should I do in this regard. do I need to use some visualisation
> software. I tried with Pymol but appending of the molecule I could not do.
> Can you help me in this matter.
> Thanks a lot
> With regards,
> --
> Deepti Lele,
> NII, New Delhi.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail:
Stony Brook, NY 11794-5115 Web:
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Received on Wed Aug 27 2008 - 06:07:48 PDT
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