If you want to dig deeper yourself, trace the atoms back to their nb
parameter indexes in the prmtop to see what overlaps.
Bill
On 7/7/17 3:06 PM, Quynh Vo wrote:
> 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 - 16:00:03 PDT
