Thanks for the advice. I will try it out. As the generation takes quite a
lot of time, I can not update you as to whether it worked or not. But as
soon as I get anything, I will keep you posted. Thanks again.
On Sat, Nov 5, 2022 at 10:59 AM David A Case <david.case.rutgers.edu> wrote:
> On Fri, Nov 04, 2022, Tanmoy Paul via AMBER wrote:
>
> >I am trying to generate topology and inpcrd files for a system that
> >contains around 400,000 atoms. Upon solvating, the atom number becomes
> >around 5,000,000.
>
> I don't have an answer, but a few comments are given below.
>
> >source leaprc.water.tip3p
> >loadamberparams /usr/local/amber16/dat/leap/parm/frcmod.ionsjc_tip3p
>
> You don't need the last line above, since it is already a part of
> leaprc.water.tip3p. This also loads standard paramters for magnesium; so
> unless you know you need different parameters, you don't need to load your
> own Mg2+ parameters.
>
> >solvatebox mol TIP3PBOX 12.0
>
> Let's try to narrow down the problem: as an experiment, try a much smaller
> buffer, say 8 Ang. instead of 12. This will lead to many fewer atoms. Do
> you still see problems? If you do, leave out the water altogether -- let's
> see if the protein system itself is leading to problems.
>
> Loading a prmtop file from Amber16 into VMD might not be the best way to
> tell if there are problems. Try running a zero-step MD (nstlim=0), and see
> if you get reasonable energies, especially (say) for the bonded terms.
>
> ....good luck....dac
>
>
--
With regards,
Tanmoy
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Received on Sat Nov 05 2022 - 17:30:03 PDT
