Re: [AMBER] problem with CpHMD

From: Roitberg,Adrian E <roitberg.ufl.edu>
Date: Tue, 21 Feb 2017 13:23:58 +0000

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 - 05:30:11 PST
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