Re: [AMBER] Tleap creates only one residue

From: David A Case <>
Date: Thu, 17 Sep 2020 08:45:26 -0400

On Wed, Sep 16, 2020, Farkhad Maksudov wrote:
>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 "***"

Note that (for Amber) mol2 files are used to describe single
residues, not polymers. If your "input mol2 file" indeed has many
modified nucleotides, I'm not sure that you can do anything to get the
prmtop file to think there are lots of residues.

You would really need to use antechamber/parmchk2 to create four mol2 files,
one each for the modified versions of A,C,G,U. Then, load those into
tleap, followed by loadPdb to load a PDB file for the whole structure.

Please note that what you describe is a very difficult problem, at least
in Amber. By going to GAFF, you are giving up on 20 years of careful
parameterization for torsional angles in standard RNA. If this is just
a "one-off" project you might be OK (see what happens when you run
simulations using the prmtop file you already have), but for a serious
project, I'd recommend using Amber atom types, and changing as little as
possible from the parameters used for standarad ribose sugars. This
will involve a lot of hand-work, and you would need to learn the details
of how force fields are implmented in Amber.

...hope this helps....dac

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Received on Thu Sep 17 2020 - 06:00:02 PDT
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