Re: [AMBER] problem with CpHMD

From: Roitberg,Adrian E <roitberg.ufl.edu>
Date: Tue, 21 Feb 2017 12:36:47 +0000

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 - 05:00:02 PST
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