Re: [AMBER] acetylate and ammoniate

From: mohammad r <>
Date: Wed, 12 Aug 2015 15:04:20 +0000 (UTC)

Thank you Mr. doctor;You mean that I should put the ACE residue to the beginning of the pdb file by a special command or adding it myself.
AlsoI used the loadPdbUsingSeq command but it stopped with errors saying that the residues are not units. I putted the ACE and NH2 residues in the beginning and end of the input sequence, respectively.Is it possible to generate the topology file with ambertools then convert it to the file which could be used in gromacs? (Indeed I want to use the ff14sb force field which doesn't exist in gromacs).Thanks, M.


     On Wednesday, August 12, 2015 5:41 PM, Jason Swails <> wrote:

 On Wed, Aug 12, 2015 at 8:23 AM, mohammad r <>

> Hi;
> How can I acetylate and ammoniate a peptide by using ambertools?Thank you,
> Mohammad.

​Assuming you are referring to the terminal caps of a peptide chain, then
you can cap the N-terminus with an ACE cap either by adding that residue to
the beginning of the PDB file or by putting that residue first if you are
using the "sequence" command in tleap.  I'm not sure if there's an easier
way when starting from a PDB file than trying to model it into the PDB
itself somehow.  (All you *really* need to add is a single atom from the
residue -- tleap will add the rest.)

​I'm not sure what you mean by "ammoniate", but it may be that the NHE cap
will do what you want (analogous to the ACE cap on the N-terminus).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 12 2015 - 08:30:04 PDT
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