Re: [AMBER] Parameters for non-standard residues

From: David A Case <>
Date: Wed, 20 Oct 2021 11:22:50 -0500

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.

>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.

>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.


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Received on Wed Oct 20 2021 - 09:30:03 PDT
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