Re: [AMBER] problem with CpHMD

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Tue, 21 Feb 2017 13:31:21 +0000

Adrian and David,



Many thanks for your advises.
I have added the line
loadamberparams frcmod.ionsjc_tip3p
and TLEAP completed without errors.

Michael
________________________________
From: Roitberg,Adrian E <roitberg.ufl.edu>
Sent: Tuesday, February 21, 2017 3:23:58 PM
To: AMBER Mailing List
Subject: Re: [AMBER] problem with CpHMD

Hi michael,
You are confusing the cphmd part of the run, that indeed does not care about the ions, with the MD part of the run.
If you have a sodium atom in your system and do not load the ion parameters, tleap has no way to know what Na+ means.

Adrian


Sent from my iPad

> On Feb 21, 2017, at 8:19 AM, Michael Shokhen <michael.shokhen.biu.ac.il> wrote:
>
> 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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Received on Tue Feb 21 2017 - 06:00:03 PST
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