Re: [AMBER] adding non-standard residue to RNA strand

From: FyD <>
Date: Tue, 12 Jul 2016 23:03:16 +0200

Dear Martina,

> I have the given mol2 generated from RED server.I tried incorporating the
> given mol2 with the RNA strand. Though the non-standard manages to load
> through leap it does not mesh with the RNA strand.
> a=loadpdb a.pdb
> OAU=loadmol2 OAU.mol2
> a=loadpdb a.pdb
> Do I need to edit the mol2 manually to lead to its successful incorporation?

If I look at your mol2/mol3 file; it looks like an "empty" mol3 file
for this _molecular_ fragment...

tail -n 5 OAU.mol2

0 0
0 0
1 0 0 0 0 0 0


the head & the tail should be described as:

P 1
O5 1
1 P O5 0 0 0 0

there is something wrong...

When describing the problem you encountered with R.E.D. Server
Development, please also provide the 'PXXXX' R.E.D. Server Development
job name in the body of your email so that we can more easily assist

Provide the PXXXX job name so that we can have a look to your data...

regards, Francois

           F.-Y. Dupradeau

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Received on Wed Jul 13 2016 - 00:00:02 PDT
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