Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output

From: Josť Daniel Martinez <jmartinez.cicbiogune.es>
Date: Wed, 27 May 2020 08:25:01 +0000

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 Josť 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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[ASOCIACION CENTRO DE INVESTIGACION COOPERATIVA EN BIOCIENCIAS] [Center of Excellence Severo Ochoa]

Center of Excellence Severo Ochoa (2017-2021)

All information and attachments included in this email are confidential and intended for the original recipient only. You must not share any part of this message with any third party. If you have received this message by mistake, please reply to let us know immediately, so we can make sure such a mistake does not happen again and delete this message from your system. We have put our efforts into ensuring that this message is free of errors and viruses but, despite our efforts, you should always scan all emails for any threats with proper software, as the sender does not accept liability for any damage inflicted by viewing the content of this email. We also would like to inform that all personal data included in this email or in the attached documentation, could be processed by ASOCIACION CENTRO DE INVESTIGACION COOPERATIVA EN BIOCIENCIAS with the aim of managing the legal relationship between the parties. If you would like to access, modify or oppose to the treatment of your data, you can contact us in writing.

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