Re: creating topology for a unique structure

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Nov 05 2018 - 10:49:48 CST

Soroush,

We really need more information than your are providing. Based on what you
have sent already, you need to spend more time with the tutorial material.
Simple re-posting the same question phrased differently will not lead to a
solution for your problem.

Some particular answers to your questions:

Atom groups are no longer used for any specific purpose. CGenFF generally
uses them to designate integer charge units, but this is just bookkeeping.
A single molecule is thus most often considered as one group - note that
this has nothing to do with alchemical transformations.

Unless you are doing an absolute solvation/binding energy calculation, you
will not be able to use the CGenFF generated topology directly for
alchemical calculations. You will have to either create a new hybrid
topology by hand or else create a patch that amends an existing topology to
include your other endpoint molecule (or else the modifications that define
it). Examples for how to do this should be in the tutorial.

On Sun, Nov 4, 2018 at 3:03 AM soroush ziaei <soroush.ziaei7337_at_gmail.com>
wrote:

> hi all,
> i have some structure that doesn't have any similar topology in charmm22
> (protein) & charmm 27 (lipid) and i have tried several servers such as,
> cgenff & swiss param, but the .rtf file generated from this method
> gathering all of atom types in one group, why?
> is there something that i might be missing?
> meanwhile, i want to use this topology in order to detect groups and atoms
> for running free energy perturbation simulation (fep)..
> what should i do?
> if someone who know the solution, i must to tell please guide me, i
> appreciate.
>
> regards,
> soroush
>

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