I partially solved my problem.
When I save system as PDB directly from leap (I.e. include “savepdb complex
test.pdb” in the leap command file), then I can see my pseudo atoms in
water molecules. Then, EPW atoms are indeed present in the prmtop file.
Alternatively, if instead I use ambpdb (ambpdb -p test.prmtop -i
test.inpcrd > test2.pdb) this produces a PDB which does NOT include
pseudoatoms EP/EPW atoms and moreover is shifted in space in all three axes
compared to test.PDB produced by leap.
Why is there such a difference between PDB files of the same system
produced by leap and ambpdb?
On Tue, 29 Nov 2022 at 16:31, David A Case <david.case.rutgers.edu> wrote:
> On Tue, Nov 29, 2022, Dmitry Suplatov via AMBER wrote:
> >
> >source leaprc.gaff
> >source leaprc.protein.ff14SB
> >source leaprc.water.tip4pew
> >HOH=TP4
> >WAT=TP4
> >complex = loadpdb protein_prep.pdb
> >solvateBox complex TIP4PEWBOX 12
> >saveamberparm complex test.prmtop test.inpcrd
> >quit
> >
> >
> >As the result, the model is built but all water molecules contain only
> >three atoms. The water pseudo atoms EW are not present anywhere in the
> >files.
>
> Are you sure? What files did you look at? Try using the "summary" command
> in parmed, followed by "printDetails :xxx", where "xxx" is the residue
> number of one of your water molecules.
>
> ...good luck....dac
>
>
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Received on Tue Nov 29 2022 - 09:00:03 PST
