On Mon, Apr 12, 2021 at 8:49 AM David A Case <david.case.rutgers.edu> wrote:
> On Mon, Apr 12, 2021, 马芳芳 wrote:
>
> >For atom: .R<Na+ 3>.A<Na+ 1> Could not find type: Na+
> >For atom: .R<Na+ 4>.A<Na+ 1> Could not find type: Na+
>
> Ions are included in the "water" leaprc files, since they depend on the
> water model you choose. So, you need to include something like
> "source leaprc.water.xxxx", where xxxx represents the water model you wish
> to use. See the Reference Manual for some more details.
>
> ...dac
>
I think the problem might be deeper than this....
> source leaprc.ff12SB
----- Source: /software/soft/amber/amber12/dat/leap/cmd/leaprc.ff12SB
it looks like you're using amber12, I would suggest upgrading to the latest
AmberTools.
> source leaprc.ff99
Could not open file leaprc.ff99: not found
> source leaprc.ions94
Could not open file leaprc.ions94: not found
> AA=loadmol2 AA-antechamber.mol2
this might be the problem: you're getting error messages loading your
leaprc files.
I think it would be best to upgrade AmberTools, then use a more modern
protein model, and then as Dave Case said, you'll need to specify your
water model. It will look like this (if you choose TIP3P).
source leaprc.protein.ff14SB
source leaprc.water.tip3p
The Amber tutorials are a good resource for system setup, for example this
one on building systems in explicit water
http://ambermd.org/tutorials/basic/tutorial7/index.php
>
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Received on Mon Apr 12 2021 - 06:30:05 PDT
