Hello,
I think I found out why AMBER gave that error. The inputs from CHARMM
should not have the extra bond between the two hydrogen atoms of water
molecules. I regenerated my psf/pdb files using Automatic PSF Builder
plugin on VMD, which does not add that extra bond. Then I converted those
files to AMBER inputs, and it works fine.
Thanks,
Sadegh Faramarzi,
Research Assistant
West Virginia University, Department of Chemistry
Email:safaramarziganjabad.mix.wvu.edu
On Wed, May 23, 2018 at 3:36 PM, Sadegh Faramarzi Ganjabad <
safaramarziganjabad.mix.wvu.edu> wrote:
> David,
>
> I'm not using top_all27_na.rtf or top_all27_prot_na.rtf. Here is the
> syntax I use on parmed
>
>
> chamber -top top_all36_lipid.rtf -param par_all36_lipid.prm -param
> par_all36m_prot.prm -param par_all36_cgenff.prm -param par_all36_na.prm
> -param ddm2.prm -param par_all36_carb.prm -param par_all36_prot_mod.prm
> -str toppar_all36_lipid_detergent.str -str ../retinal-depro.str -toppar
> toppar_water_ions_fixed.str -psf all-ion.psf -crd all-ion_new.pdb -nocmap
> -box 75.4,75.13,83.8
>
> I checked the files above, they don't have the error that top_all27_na.rtf
> has. Interestingly. I have tested the same param/topology files for another
> system for which the water molecules are generated with VMD. They work
> well. But for the system generated with CHARM-GUI website I get that SHAKEH
> error for water molecules.
>
> I'm using AmberTools 18. I'm sending you all the files I use. I looked at
> the pdb file, atoms with indices 23639, 23638, 23640 are the first water
> molecule that appears on pdb file after the bilayer atoms.
>
>
>
> Date: Tue, 22 May 2018 15:53:54 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3
> water model
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20180522195354.5nge63p6hrxxgdk2.vpn-client-172-16-8-12.
> rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> > On Mon, May 21, 2018, Sadegh Faramarzi Ganjabad wrote:
> > >
> > > I have converted CHARMM inputs to AMBER inputs. Not sure why but there
> are
> > > extra bonds between two hydrogen atoms in the water molecules in the
> > > original CHARMM files. When I try to run the AMBER inputs it complains
> > > about those extra bonds. Here is the error I get
> > >
> > > Hydrogen atom 23639 appears to have multiple bonds to atoms 23638 and
> > > 23640 which is illegal for SHAKEH.
> Please see the recent mailing list entry about a similar problem. Are
> you using top_all27_na.rtf or top_all27_prot_na.rtf? If, so that post
> might
> have help for you.
>
> If the hydrogens above are really in water, can you say exactly how you
> convert CHARMM to AMBER inputs? Which version of AmberTools do you
> have?
>
> ...thx...dac
>
> Thanks,
> Sadegh Faramarzi,
> Research Assistant
> West Virginia University, Department of Chemistry
> Email:safaramarziganjabad.mix.wvu.edu
>
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Received on Mon May 28 2018 - 14:00:03 PDT
