Re: [AMBER] acetylate and ammoniate

From: Jason Swails <jason.swails.gmail.com> Date: Thu, 13 Aug 2015 07:23:38 -0400

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
> On Aug 13, 2015, at 3:06 AM, mohammad r <mohammad.r0325.yahoo.com> wrote:
> 
> 
> 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 <david.case.rutgers.edu> 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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