On Wed, May 27, 2020 at 4:25 AM José Daniel Martinez
<jmartinez.cicbiogune.es> wrote:
>
> Hi Daniel!
> I double checked the preparation of the topology file as you mentioned, and found that I used gaff2 parameters, instead of gaff... And the parameters output by 'atominfo' are the same as in the gaff2.dat file.
> My mistake, sorry.
>
> Thanks for your help!
Happy to help out a fellow Dan :-)
>
> Best,
>
> Dan.
> ________________________________
> De: Daniel Roe <daniel.r.roe.gmail.com>
> Enviado: martes, 26 de mayo de 2020 17:23
> Para: AMBER Mailing List <amber.ambermd.org>
> Asunto: Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output
>
> Hi,
>
> Cpptraj back-calculates the Lennard-Jones parameters from the
> <type>-<type> A and B present in the topology file. I just
> double-checked that cpptraj is giving the correct values by
> parameterizing galactose with antechamber:
>
> ```
> > atoms .%h1
> [atoms .%h1]
> #Atom Name #Res Name #Mol Type Charge Mass GBradius El rVDW eVDW
> 16 H4 1 GAL 1 h1 0.1087 1.0080 1.3000 H 1.3870 0.0157
> 17 H5 1 GAL 1 h1 0.0617 1.0080 1.3000 H 1.3870 0.0157
> ```
>
> Without knowing how you built your topology there's really no way of
> telling why you're getting the values you did. You'd have to provide
> the exact details. What version of cpptraj are you using?
>
> -Dan
>
> On Sat, May 23, 2020 at 8:18 AM José Daniel Martinez
> <jmartinez.cicbiogune.es> wrote:
> >
> > Hi everyone!
> >
> > I am wondering why the LJ parameters in the gaff.dat file are different from those output by the CPPTRAJ command 'atominfo'. For instance, the parameters for 'h1' as specified in the .dat file, are:
> > h1 1.3870 0.0157
> > However, when I call 'atominfo' for my molecule, the output VdW parameters for a 'h1' are:
> > rWDW = 1.3593
> > eVDW = 0.0208
> >
> > Does anybody know what is going on here?
> >
> > Thanks!
> >
> > Dan.
> >
> >
> >
> >
> >
> > [ASOCIACION CENTRO DE INVESTIGACION COOPERATIVA EN BIOCIENCIAS] [Center of Excellence Severo Ochoa]
> >
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> >
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> [ASOCIACION CENTRO DE INVESTIGACION COOPERATIVA EN BIOCIENCIAS] [Center of Excellence Severo Ochoa]
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Received on Wed May 27 2020 - 08:30:02 PDT
