Sorry! It did not work. The error remains the same. Any other tips?
On Sat, Nov 5, 2022 at 8:26 PM Tanmoy Paul <tanmoyp635.gmail.com> wrote:
> 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
>
--
With regards,
Tanmoy
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Received on Sun Nov 06 2022 - 03:00:03 PST
