Re: [AMBER] problem with CpHMD

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Tue, 21 Feb 2017 13:19:07 +0000

Dear Adrian,


In my MD simulations in explicit water solvent

I usually use in TLEAP the

loadamberparams frcmod.ionsjc_tip3p

As I understood from the corresponding Amber tutorial

the CpHMD is adopted for implicit dielectric continuum solvent model.

Is the command loadamberparams frcmod.ionsjc_tip3p

relevant for implicit sovent in CpHMD also ?


Thank you,

Michael



*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
________________________________
From: Roitberg,Adrian E <roitberg.ufl.edu>
Sent: Tuesday, February 21, 2017 2:36:47 PM
To: AMBER Mailing List
Subject: Re: [AMBER] problem with CpHMD

Have you loaded the leaprc files for ions ?
Adrian

Sent from my iPad

> On Feb 21, 2017, at 7:04 AM, Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
>
>
>
> Dear Amber experts,
>
> I have on my Linux server Amber16 and AmberTools16.
> I want to use constant pH molecular Dynamics (CpHMD)
> for identification of pKa of His residues of my protein.
> I have followed the AMBER tutorial:
> TUTORIAL A18: Constant pH Molecular Dynamics Example - Calculating pKas for titratable side chains in HEWL<http://ambermd.org/tutorials/advanced/tutorial18/index.htm>
> My protein chelates the Na cation.
> This circumstance causes the problem in TLEAP.
> Please find details below.
>
> What changes and corrections should be added to my tleap.in file
> in order TLEAP can accept Na cation ?
>
> Thank you,
> Michael
>
> I have ran the command: tleap f tleap.in
> Where the input file tleap.in is
>
>
> source leaprc.constph
> # Load the PDBs
> mc = loadPDB eq_md15_nh.pdb
>
> # Save topology files
> saveAmberParm mc mc.parm7 mc.rst7
>
> # Quit
> quit
>
> Computer reported the error:
>
> Building topology.
> Building atom parameters.
> For atom: .R<NA 376>.A<NA 1> Could not find vdW (or other) parameters for type: Na+
> Parameter file was not saved.
>
>
>
>
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> AMBER.ambermd.org
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Received on Tue Feb 21 2017 - 05:30:08 PST
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