Re: [AMBER] tleap problem with spc water

From: Carlos Simmerling via AMBER <>
Date: Mon, 20 Jun 2022 10:51:48 -0400

Amber 16 is quite old, I would suggest trying to update to the
current AmberTools if possible. Some of the locations of water parameters
have been changed, and in the old setup it could lead to problems as you
have seen. Now all of the water parameters should be with the individual
water files.

On Mon, Jun 20, 2022 at 10:03 AM Giulia Sormani via AMBER <>

> Good morning everyone,
> I already sent similar message some time ago, I haven't receive any reply,
> so I try again..
> I am simulating an organic molecule (DFO) in a spce water box. I got the
> mol and the frcmod file from antechamber, so I am ready to run tleap.
> Here is the input file for tleap:
> "
> source leaprc.gaff
> source leaprc.water.spce
> mol = loadmol2 DFO.mol
> solvatebox mol SPCBOX 17.0
> loadamberparams frcmod.spce
> loadamberparams DFO.frcmod
> addIons mol NA 2
> saveoff mol dfo.lib
> quit
> "
> For each water H, I get the following error:
> For atom: .R<WAT 2>.A<H1 2> Could not find vdW (or other) parameters for
> type: HW
> I don't understand why this happens since the leaprc.water.spce and
> frcmod.spce files are correctly loaded.
> Curiously this message disappear if I add as a first line
> source leaprc.protein.ff14SB
> which is the protein FF, so I don't see why it is related to water.
> Can anyone help?
> Giulia
> PS output of tleap in the attachment
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Received on Thu Aug 04 2022 - 13:32:29 PDT
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