Re: AMBER: Modified RNA Bases

From: Raviprasad Aduri <>
Date: Tue, 27 Sep 2005 13:22:45 -0400

Dear Prof.Francois,

Thank you very much for your prompt reply. The problem I am facing is that
I don't have a starting PDB file of the nucleoside to convert into .mol2
format. I am working on some modifications for which there are no available
PDB files. I made the base with the methyl attached using "Gauss View" and
did the calculations. Now I am just wondering if there is any way I can
strip of the methyl group and add the sugar part to the final prepin file I
get from the antechamber. I hope I am clear in my question.

Thank you for spending your precious time.
Raviprasad Aduri

At 01:45 AM 9/27/2005, you wrote:
>Quoting Raviprasad Aduri <>:
> > I am trying to develop parameters for a modified RNA base. I did the
> > Gaussian calculations on the base with a methyl group attached in place of
> > the Sugar moiety. I did the multi-orientation fit using RED II and then
> > used the sugar charge constraint on the methyl group in the RESP fitting.
> > Now my question is how do I make the "prepin" file and the "frcmod" file
> > for the whole nucleoside.
>You can also use Tripos .mol2 file. See
>In this case, you have to build the 'nucleoside.mol2' file (this is done
>automatically in R.E.D.-III)
>The Cart. coord in this .mol2 does not have to be 'perfect': They can be
>'bizarre' ;-) since only the topology matters...
>You can build a Tripos file from a PDB file for instance using babel...
>regards, Francois
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Sep 27 2005 - 18:53:00 PDT
Custom Search