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!
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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Received on Wed May 27 2020 - 01:30:02 PDT
