Hi,
I added “jfastw=4” to the mdin file for energy minimization of added water and ions.
For the mdin files for heating up system under constant V and relaxing the system under constant P, I used “ntc=2, ntf=2, jfastw=4, noshakemask=‘:WAT’ “.
This worked. Thank you so much for your help!
Best,
Kiriko
From: Terai, Kiriko via AMBER <amber.ambermd.org>
Date: Thursday, October 2, 2025 at 12:37 PM
To: Masoud Keramati <keramati.m.northeastern.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Solvate with SPC/Fw water
Hi,
I have "set default FlexibleWater on” in my tleap input, but not "Jfastw=4” in the .mdin file.
I will try ""Jfastw=4”.
Thank you,
Kiriko
From: Masoud Keramati <keramati.m.northeastern.edu>
Date: Thursday, October 2, 2025 at 12:32 PM
To: Terai, Kiriko <kirikot.unc.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: Solvate with SPC/Fw water
You don't often get email from keramati.m@northeastern.edu. Learn why this is important<
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I think in tleap you need use:
set default FlexibleWater on
And in you .mdin file:
Jfastw=4
________________________________
From: Terai, Kiriko <kirikot.unc.edu>
Sent: Thursday, October 2, 2025 12:16
To: Masoud Keramati <keramati.m.northeastern.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Solvate with SPC/Fw water
Hi,
These are the water molecules in the pdb file that I obtain from running tleap:
ATOM 78 O WAT 2 12.254 8.622 17.398 1.00 0.00
ATOM 79 H1 WAT 2 12.174 7.707 17.127 1.00 0.00
ATOM 80 H2 WAT 2 11.841 9.118 16.691 1.00 0.00
TER
ATOM 81 O WAT 3 2.812 5.672 13.940 1.00 0.00
ATOM 82 H1 WAT 3 1.923 6.013 13.838 1.00 0.00
ATOM 83 H2 WAT 3 3.096 5.472 13.048 1.00 0.00
TER
ATOM 84 O WAT 4 4.988 4.255 14.974 1.00 0.00
ATOM 85 H1 WAT 4 5.095 5.155 15.281 1.00 0.00
ATOM 86 H2 WAT 4 4.077 4.207 14.684 1.00 0.00
Thank you,
Kiriko
From: Masoud Keramati <keramati.m.northeastern.edu>
Date: Thursday, October 2, 2025 at 12:12 PM
To: Terai, Kiriko <kirikot.unc.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: Solvate with SPC/Fw water
You don't often get email from keramati.m@northeastern.edu. Learn why this is important<
https://aka.ms/LearnAboutSenderIdentification>
Hi,
Check if the name of water molecules/atoms are the expected names by AMBER ( 'WAT', 'O', 'H1', and 'H2').
Best,
Masoud
________________________________
From: Terai, Kiriko via AMBER <amber.ambermd.org>
Sent: Thursday, October 2, 2025 12:02
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Solvate with SPC/Fw water
Hello,
I’m running into an error when relaxing a system solvated with SPC/Fw water model. In the first step (energy minimization of added water and ions), the job stops with:
Error: Fast 3-point water residue, name and bond data incorrect!
tleap completed without fatal errors and produced rst7 and parm7 files, but I suspect something went wrong in how SPC/Fw waters were set up. I’ve attached my tleap input and tleap log. Could you please provide me some guidance for this issue?
Thank you,
Kiriko
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Received on Thu Oct 02 2025 - 13:00:03 PDT
