Hi all,
I would like to prepare .parm and .top files for my B-DNA model (1bna PDB code) using ff-nucleic-OL15 (OL Force Field Refinement for RNA and DNA Simulations (upol.cz)<
https://fch.upol.cz/ff_ol/>) with AMBER 16. I have used the following input for tleap and have modified the pdb input file for both atom types (O’3H and O’5H) and residue names (DC5 and DG3 in each strand) at 3’ and 5’ terminals.
I got the following error about atom types (for free hydroxyl terminals at 3’ and 5’ ends).
Can anyone help me with this?
I appreciate any help/suggestion
Cheers
Zahra
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WARNING: The unperturbed charge of the unit: -12.000000 is not zero.
FATAL: Atom .R<DC 1>.A<HO5' 31> does not have a type.
FATAL: Atom .R<DG 12>.A<HO3' 34> does not have a type.
FATAL: Atom .R<DC 13>.A<HO5' 31> does not have a type.
FATAL: Atom .R<DG 24>.A<HO3' 34> does not have a type.
Failed to generate parameters
tleap input:
source leaprc.ff14SB
source leaprc.water.tip3p
set default pbradii mbondi2
loadAmberParams frcmod.ionsjc_tip3p
addAtomTypes {
{ "C7" "C" "sp3" }
{ "CJ" "C" "sp3" }
{ "C1" "C" "sp2" }
{ "C2" "C" "sp2" }
}
loadoff ff-nucleic-OL15.lib
loadamberparams ff-nucleic-OL15.frcmod
model = loadpdb modeldna.pdb
check model
solvatebox model TIP3PBOX 10.0 2.00
addions model Na+ 12
saveamberparm model model.top model.rst
savepdb model model_leap.pdb
quit
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Received on Tue Sep 07 2021 - 04:00:03 PDT
