Thanks David and Bill.
Yes I'm a little bit concern because all of the atom types have different LJ parameters. The individual molecule has C and H in common but I reparametrized them to have different LJ parameters and named them differently too.
Also if I prepared the prmtop and inpcrd using prep-link-edit-parm I would get 8 for NTYPES (NTYPES=7 with amber14). I prefer LEaP though so I'd like to iron out this discrepancy.
Thanks again!
On Friday, July 7, 2017 6:41 AM, David Case <david.case.rutgers.edu> wrote:
On Thu, Jul 06, 2017, Quynh Vo wrote:
> I have 2 non standard molecules, one with 6 unique atom types (44
> atoms total), the other one is an alkane with 2 atom types (38 atoms
> total). When I generate prmtop and inpcrd for the mixture of these 2
> molecules, xleap (tleap) only recognized 7 distinct atom types (NTYPES
> = 7 in prmtop). It reports NTYPES correctly for individual molecule. I
> looked at the frcmod file and all atom types have different LJ potential
> parameters. So I wonder why the discrepancy and if it would affect the
> simulations at all. I'm using Amber/AmberTool 14.
LEaP will "merge" (or "combine") atom types when they have the same
Lennard Jones parameters. That is, NTYPES is an internal variable that
keeps track of the number of unique LJ parameters in the combined system.
This will often be smaller than the sum of the NTYPES variables in
subsystems. It seems unlikely that you have any problem here.
...hope this helps....dac
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Received on Fri Jul 07 2017 - 15:30:02 PDT
