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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 07 2021 - 05:00:02 PDT
