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

From: FyD <>
Date: Sat, 13 Oct 2012 12:42:41 +0200

Dear Sajeewa Pemasinghe,

the prep, off and mol2 file formats have the same role: they are used
to handle FF libraries. prep is the old format designed with the
'plep' program; off was introduced with LEaP; then came the mol2 file
format. We will use soon the mol3 file format in R.E.D.

Nowadays R.E.D. generates only mol2 files and no prep file:

When one wants to create a FF library for a new amino-acid; one often
need the corresponding fragment obtained from a dipeptide:
Other fragments (terminal ones) can also be designed:

The different fragments can be generated in a single step by now:

regards, Francois

> 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.

AMBER mailing list
Received on Sat Oct 13 2012 - 04:00:02 PDT
Custom Search