Dear David,
I have checked the prmtop file for the atom 2413 belonging to boron atom. I
think the parameters are correct.
The output from parmed looks like this
=======================================
['parmed.in']
Reading actions from parmed.in
The mask .2413 matches 1 atoms:
ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth
Mass Charge GB Radius GB Screen
2413 161 SEB B1 B 5 1.9800
0.0340 10.8100 1.0825 1.5000 0.8000
Done!
=======================================
I also add an AddAtomTypes command in leap, but the generated prmtop file
is the same as the previous one.
My tleap script looks like this
=======================================
#!/bin/bash
source leaprc.protein.ff14SB
source leaprc.gaff
loadAmberPrep SEB.prepin
loadAmberParams frcmod2.SEB
loadAmberParams frcmod1.SEB
addAtomTypes { { "B1" "B" "sp3" } }
mol = loadpdb test.pdb
charge mol
check mol
saveamberparm mol test.prmtop test.rst7
quit
=======================================
Best wishes,
Bodee
On Fri, May 11, 2018 at 1:48 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Thu, May 10, 2018, Bodee Nutho wrote:
> >
> > I'm trying to perform QM/MM MD on a boron-containing compound.
> > I did perform an equilibration of the complex for 1-ns using classical MD
> > simulation. Everything seems to be fine with this classical MD.
> >
> > After that, I switched from running classical MD to QM/MM MD using PM6
> > Hamiltonian. I have found the problem with the reading of boron atom in
> > which boron atom turned to be an unknown element.
> > How should I solve this problem?
>
> Can you examine your prmtop file (either with parmed or just with a text
> editor): what is the atom name for atom 2413? Easiest to do would be
> run parmed, and issue the command "printDetails .2413": see if the name,
> mass, atomic number, etc. are correct.
>
> The underlying problem is probably in how you made the prmtop file in
> the first place, perhaps lacking an "AddAtomType" command in leap. MM
> calculations don't really care about the atomic number, but QM
> calculations do. Probably just editing the ATOMIC_NUMBER section of the
> prmtop file to provide the proper atomic number will help.
>
> ...good luck....dac
>
>
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>
--
Bodee Nutho
Program in Biotechnology
17th floor, MHMK Building
Chulalongkorn University
Bangkok, THAILAND 10330
Tel: +66 (0)83 547 3066
Email: b.nutho.gmail.com
* <swaratchada.gmail.com>*
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Received on Thu May 10 2018 - 19:30:02 PDT
