[gmx-users] CLARIFICATION IN RESIDUE TOPOLOGY FILE

[Mark Abraham]

On Tue, Jan 17, 2017 at 3:55 AM Subashini .K <subashinik at hotmail.com> wrote:

> Hi gromacs users,
>
>
> While preparing the .rtp file, what does the third and fourth column
> describe?
>
> ; Methane
> [ CH4 ]
> [ atoms ]
>
>
> C      opls_138    -0.240     1
>
> H1     opls_140     0.060     1
>
> H2     opls_140     0.060     1
>
> H3     opls_140     0.060     1
>
> H4     opls_140     0.060     1
>
>
> Does the number -0.240 indicate the charge of Carbon? Does it indicate
> Mulliken charge/electrostatic potential charge? How to calculate it for any
> arbitrary organic molecule?
>

It represents an effective partial charge. How it is derived varies with
the force field. Please see a good textbook on molecular mechanics, and
then get some experience with standard simulations before attempting to
parameterize new things.

Mark


>
> Thanks,
>
> Subashini.K
>
>
>
>
>
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