Re: [AMBER] How Can I modify a amino acid in Amber?

From: Sajeewa Pemasinghe <>
Date: Sat, 13 Oct 2012 03:48:49 -0400

Hi Yan,

As far as I know this goes as a non-standard residue. So you give your
modified amino acid a new three letter name in the pdb file. But as AMBER
tleap or xleap doesn't understand the new residue (coz it is not in the
standard list of residues in the force fields loaded) you have to create a
.frcmod file and a .prep file for the new residue. To create the .frcmod
you have to first build the structure of the modified amino acid using a
software like Gaussian, then optimize the structure and get the optimized
parameters. Using these parameters you can create a .frcmod file (Google to
check for the format of the .frcmod file, in some cases you can use
Antechamber to do this for you) for the new residue. To create the .prep
file you will need the charges for the new residue which you can obtain
using (

Once you have the .frcmod and the .prep files

1) As usual you do tleap -s -f leaprc.ff99SB (whatever the force field you
wanna use)

2) loadamberparams xxx.frcmod (choose a name and replace xxx)

3) loadamberprep xxx.prep (choose a name and replace xxx)

4) a=loadpdb xxx.pdb (in this pdb you should have the new name for the
modified amino acid, you don't have to have the methyl group as tleap will
do it for you according to the parameters you specified in the .frcmod file)

Hope this helps

Sajeewa Dewage

On Fri, Oct 12, 2012 at 10:17 PM, Changqing Yan <>wrote:

> Hi all,
> If I want to methylated one amino acid in a peptide sequence, for example I
> want to methylate VAL residue in TSPNR(N-Methylated)VGDE. What should I do?
> Thanks in adavance.
> C.Q.
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Received on Sat Oct 13 2012 - 01:00:03 PDT
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