Re: [AMBER] Parameters for non-standard residues

From: Dr. Anselm Horn <>
Date: Thu, 21 Oct 2021 16:21:57 +0200


> On Tue, Oct 19, 2021, Nagar, Hemant wrote:
>> I went through the tutorial of antechamber to generate force field
>> parameter for nonstandard residues. I have following questions-
>> a) how to generate mol2 file for two conformations(alpha and beta)?
>> These two conformation are for the particular molecule that is given in
>> the tutorial or we need to generate these two conformation for every
>> nonstandard fragment?
> I think that the alpha/beta stuff is specific to the example being used
> there.

alpha/beta conformations are normally used for amino-acid-like residues.
You can use any molecular structure tool to create initial
conformations. For other compounds, one could generate different
conformations accordingly.

>> I found following command on AMBER tutorials to generate mol2 files-
>> antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc
>> -s 2
>> I can save my nonstandard residue in different file and using this
>> command
>> I can generate mol2 file but how I can generate two mol2 files?
> Run antechamber twice, once for each residue.  Don't try to put more than
> one residue into any single mol2 file.

antechamber works like a conversion tool here, it does not generate any
new conformations. Furthermore, as David said, treat one non-standard
residue at a time.

>> b) After following the procedure that is given in the tutorial of
>> antechamber, how I can generate library file for that particular
>> nonstandard residue?
> You can use the loadMol2/saveOff combination in tleap to create a library
> file.  The (only?) advantage of the library format is that is has the
> connection information.

The library file may also contain additional force field parameters for
your system.
Essentially, the library files are just easier to handle, but there is
no effective difference to a pair of prep/frcmod files.

A final note:
Although the friendly tools within Amber enable the user to easily
create force field parameters, it is up to the user to decide whether
the parameters created are applicable and useful for the intended
project. Parameterization is still an advanced task in MD. And as
always, a closer look into the original literature cited e.g. in the
Amber manual may be very helpful here.

All the best,


Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg

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Received on Thu Oct 21 2021 - 07:30:02 PDT
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