Re: [AMBER] acetylate and ammoniate

From: mohammad r <>
Date: Thu, 13 Aug 2015 07:06:16 +0000 (UTC)

Thank you David;I have a problem with xleap. When I start xleap, I cannot use the "pulldown" items above the window. When I keep the mouse button down and move the mouse to highlight the item, it would'nt get highlighted. i=I don't know if it is installed correctly or not.As I am new to ambertools, do you know any tutorial or text book which I can use to start working with?Is it possible to generate topology file only by using ambertools?thank you, M.


     On Wednesday, August 12, 2015 8:09 PM, David A Case <> wrote:

 On Wed, Aug 12, 2015, mohammad r wrote:

> You mean that I should put the ACE residue to the
> beginning of the pdb file by a special command or adding it myself.

If you have a particular structure of a peptide (in PDB format) and you wish
to add capping groups to it, that is a bit tricky.  You would need to load the
peptide structure into xleap (or some other modeling program), and graphically
add the additional atoms, save the pdb file.  Probably then edit the resulting
PDB file to make sure that the atom and residue names exactly match those in
the Amber residue libraries.

If you just need an arbitrary structure, you can use a command like this
in LEaP:

peptide = sequence { ACE ALA LYS GLU NME }

> I used the loadPdbUsingSeq command but it stopped with errors saying
> that the residues are not units.

It is generally much more helpful to give both the exact command you used in
tleap and the exact error message.  But what you are probably trying to do is
more difficult than just using loadPdbUsingSeq.

...good luck....dac

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