Dear AMBER network,
I am trying to solvate my protein system using a four-point water model
like Tip4pew or OPC.
I use the following instruction file for leap:
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.
What am I doing wrong?
Please comment.
All the best,
Dmitry
On Mon 14. Nov 2022 at 10:48, Mehdi D. Davari via AMBER <amber.ambermd.org>
wrote:
> Dear AMBER Network,
>
> We are currently hiring postdoctoral and PhD student researchers in
> computational chemistry to my team at The Leibniz Institute of Plant
> Biochemistry (IPB) in Halle (Saale), Germany. Our group studies protein
> engineering and designs new enzymes using a wide range of computational
> approaches, including QM, MD, QM/MM, structural bioinformatics and machine
> learning approaches.
>
> Further information including an application link can be found here:
> https://www.ipb-halle.de/en/career/
>
>
> Many thanks,
> Mehdi Davari
>
>
> *Dr. Mehdi D. Davari Research group leader in Computational Chemistry*
>
> Tel:
> E-Mail:
>
> +49 345 5582 1360
>
> Mehdi.Davari.ipb-halle.de
>
> *Leibniz-Institut für Pflanzenbiochemie*
>
> Weinberg 3 | 06120 Halle | Deutschland
> <https://www.google.com/maps/search/Weinberg+3+%7C+06120+Halle+%7C+Deutschland?entry=gmail&source=g>
> Tel. +49 345 5582 0 | www.ipb-halle.de
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Received on Tue Nov 29 2022 - 06:30:02 PST
