I am unsure how to make an input pdf file, but would a text file be okay to attach with what xleap shows me when I put in the commands?
The commands that I implement in xleap are:
1.) source leaprc.gaff
2.) source leaprc.water.tip3p (It does say ERROR: syntax error Couldn't scan NUMBER from (+)
3.) I then load in two library files that I made pvx7.lib and hvx7.lib and load in my pdb file. It adds 2H/lone pairs, but recognizes all the atoms in the pdb file.
After this I solvate the box with
4.) solvatebox solux TIP3PBOX 8.0 wherein it tells me that it uses the default radius for O. It adds 539 water residues
I checked the charge with
5.) charge solux and it is neutral in charge.
Finally, I try to
6.) saveamberparm solux_wat.prmtop solux_wat.inpcrd
It builds the topology and builds the atom parameters then lists that it can't find vdW or other parameters for type OW, HW and HW for all but 2 waters and then says
Parameter file was not saved.
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Thursday, February 25, 2021 2:04 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] tip3p water model in amber14
On Thu, Feb 25, 2021, Swisher, Justin S wrote:
>My apologies! I didn't see this reply until just now. I'm not used to this
>interface yet.
>
> 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
We need to see the complete set of commands you gave to leap. If you can
create a small input pdb file that illustrates the problem, that would help
as well.
....dac
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Received on Thu Feb 25 2021 - 16:30:03 PST
