This explains a lot!
Thank you for your response and advice!
Farkhad
On Thu, Sep 17, 2020 at 8:45 AM David A Case <david.case.rutgers.edu> wrote:
> 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 - 13:30:02 PDT
