Hello everyone,
I just realized the difference arises due to hydrogens, as the original RNA
structure has only heavy atoms.
Thanks ,
Mandar Kulkarni
On Wed, Jul 7, 2021 at 1:47 PM Mandar Kulkarni <
mandar.kulkarni.chem.gmail.com> wrote:
> Hello Everyone,
>
> I am using AMBERTOOLS21 and GROMACS2019.6. I understand this is not
> exactly an AMBERTOOLS issue, but I am trying to understand the difference
> in energies as shown below.
>
> I am comparing single point MM energies for UUCG tetraloop structure from
> two different approaches: chiOL3 FF for Gromacs(
> https://fch.upol.cz/ff_ol/gromacs.php) and tleap+chiOL3+ACPYPE method.
> tleap + ACPYPE commands are shown below:
>
> cat > tleap.in <<EOF
> source leaprc.RNA.OL3
> rna = loadpdb uucg_cano.pdb
> check rna
> saveamberparm rna rna.prmtop rna.inpcrd
> quit
> EOF
>
> tleap -s -f tleap.in
>
> acpype.py -x rna.inpcrd -p rna.prmtop
>
> I observed the differences in energy terms for the same structure.
>
> chiOL3 GROMACS FF:
> Bond str angles dihedral LJ-14 coulomb-14 LJ
> coulomb total
> 783.149536 360.543457 737.361735 345.390991 -4339.620605 -59.470943
> 1003.757202
>
> tleap+ACPYPE:
> Bond str angles dihedral LJ-14 coulomb-14 LJ
> coulomb total
> 83.940788 1247.141724 750.041122 516.577026 -4350.560547 292.629639
> 1183.106689
>
> I look forward to your suggestions, thanks in advance.
>
> Best Regards,
> Mandar Kulkarni
>
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Received on Wed Jul 07 2021 - 07:30:02 PDT
