Re: [AMBER] tleap problem with spc water

From: Petr Stadlbauer via AMBER <>
Date: Mon, 20 Jun 2022 19:14:48 +0200

Dear Giulia,

the leap output file you attached does not show the same procedure as
the protocol you provided, so it is rather difficult to find out where
the problem was. Aren't the water molecules already present in your
input mol2 file? If so, I suggest you change their name in the file
from WAT to SPC, it might help. And if so, you need to set the box,


po 20. 6. 2022 v 16:03 odesílatel Giulia Sormani via AMBER
<> napsal:
> 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 - 13:32:32 PDT
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