[AMBER] Tleap creates only one residue

From: Farkhad Maksudov <farkhad.maksudov.gmail.com>
Date: Wed, 16 Sep 2020 21:43:58 -0400

Dear Amber developers and users,

I am trying to create topology and coordinate files for RNA containing
modifications in ribose sugars of nucleoside. To reach this aim I am
following recommendations from this tutorial
I calculated partial charges,
then I obtained missing parameters using parmchk2 utility.
After that I loaded mol2 file (containing coordinates, charges and residue
names) and frcmod file into tleap program and using GAFF force field got
prmtop file for my system. But for some reason in the output topology file
RNA is represented as only one large residue named "***" instead of a
number of separate residues (such as A, C, G and U as it is in input mol2

My question is: Why did tleap put all atoms into one residue? And how can I
fix my prmtop file or make a new one with the correct number of residues?

Any idea will be appreciated.

Thank you in advance,
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Received on Wed Sep 16 2020 - 19:00:04 PDT
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