My apologies! I didn't see this reply until just now. I'm not used to this interface yet.
The error itself displays in xleap immediately after I try to saveamberparm it reads off lines of text saying that specific error message.
saveamberparm solux solux_wat.prmtop solux_wat.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<WAT 3>.A<O 1> Could not find vdW (or other) parameters for type: OW
For atom: .R<WAT 3>.A<H1 2> Could not find vdW (or other) parameters for type: HW
For atom: .R<WAT 3>.A<H2 3> Could not find vdW (or other) parameters for type: HW
For atom: .R<WAT 4>.A<O 1> Could not find vdW (or other) parameters for type: OW
For atom: .R<WAT 4>.A<H1 2> Could not find vdW (or other) parameters for type: HW
For atom: .R<WAT 4>.A<H2 3> Could not find vdW (or other) parameters for type: HW
For atom: .R<WAT 5>.A<O 1> Could not find vdW (or other) parameters for type: OW
For atom: .R<WAT 5>.A<H1 2> Could not find vdW (or other) parameters for type: HW
For atom: .R<WAT 5>.A<H2 3> Could not find vdW (or other) parameters for type: HW
For atom: .R<WAT 6>.A<O 1> Could not find vdW (or other) parameters for type: OW
For atom: .R<WAT 6>.A<H1 2> Could not find vdW (or other) parameters for type: HW
For atom: .R<WAT 6>.A<H2 3> Could not find vdW (or other) parameters for type: HW
For atom: .R<WAT 7>.A<O 1> Could not find vdW (or other) parameters for type: OW
For atom: .R<WAT 7>.A<H1 2> Could not find vdW (or other) parameters for type: HW
For atom: .R<WAT 7>.A<H2 3> Could not find vdW (or other) parameters for type: HW
For atom: .R<WAT 8>.A<O 1> Could not find vdW (or other) parameters for type: OW
For atom: .R<WAT 8>.A<H1 2> Could not find vdW (or other) parameters for type: HW
It reads this for every water molecule except WAT 1 and WAT 2 (which I just noticed)
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Friday, February 19, 2021 11:33 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] tip3p water model in amber14
where are you seeing this error when you try to save? it is true that the
TIP3P water model does not include vdw on the H atom s(but it does on the
O).
this is the way the water model was developed and it should not cause an
error.
On Fri, Feb 19, 2021 at 11:48 AM Swisher, Justin S <
Swisher122.live.missouristate.edu> wrote:
> Hi,
>
> I'm a grad student that is rather new to using the amber program I've been
> working with it for several months now and I have been able to use
> tutorials to solve most of the issues that I'm coming across, but this
> issue I haven't been able to find an answer to and it deals with xleap. I'm
> able to solvate my molecule of interest, but when I go to save the prmtop
> and inpcrd files it says the the vDw information or some other information
> is missing from the oxygen and hydrogens in the water atoms. I am loading
> in the tip3p forcefield and it gives no errors when I load in that
> forcefield file it's only when I try to save it that this issue appears and
> I'm confused as to why there would be missing information in the forcefield
> file if it's solvating the molecule in the first place.
>
> I'm just wondering why this error would be occurring. I appreciate all
> insight you all might have in solving this issue, hopefully I have
> described the problem well enough.
>
> Thank you!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 25 2021 - 11:00:03 PST
