[gmx-users] Charges and Antechamber

[Sergio Manzetti]

Thanks, in which file do you add your residue, do you have an example? 

Thanks! 

Sergio Manzetti 

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[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
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From: "João Henriques" <joao.m.a.henriques at gmail.com> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Tuesday, October 3, 2017 4:33:55 PM 
Subject: Re: [gmx-users] Charges and Antechamber 

I just left work and I'm terrible with typing on the phone, so please bear 
with me. 

Since I mostly work with proteins and modified residues it was always worth 
it for me to edit the actual FF instead of making an itp by hand. This way 
I let pdb2gmx do the tedious work of building the topology for myself. I 
simply give it a structure and it does its magic. Is it less work? Probably 
not, since editing a FF is not exactly the simplest of tasks and requires a 
lot of attention and knowledge about what is where in the many files that 
come in a FF folder. Still, I find it to have more pros than cons. 

To summarize, I don't build the topology. I add my custom residue to the FF 
and let pdb2gmx figure the rest out. 

Hope it made sense, 
Cheers, 
João 

On Oct 3, 2017 3:53 PM, "Sergio Manzetti" <sergio.manzetti at fjordforsk.no> 
wrote: 

Thanks Joao, I am on the way with the QM part, but making the topology for 
GMX is a little bit more complicated. I thought of generating one with 
ANTECHAMBER Of a neutral species, then edit the topology itp file manually, 
but the propers are quite complex to re-edit. 

How did you get around this part? 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ 
| ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ 
| FAP ] 



From: "João Henriques" <joao.m.a.henriques at gmail.com> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Tuesday, October 3, 2017 3:50:55 PM 
Subject: Re: [gmx-users] Charges and Antechamber 

Hi! 

If your goal is to generate the atomic partial charges for a new 
residue/molecule (not existing in the FF you are interested in using), then 
doing the QM calculations is a must in most cases. For example, AMBER FFs 
have a well documented and specific recipe you can easily follow, which 
involves deriving the electrostatic potential from QM calculations at a 
specific level of theory + basis sets and then using the RESP fit procedure. 

Cornell, Wendy D., et al. "A second generation force field for the 
simulation of proteins, nucleic acids, and organic molecules." Journal of 
the American Chemical Society 117.19 (1995): 5179-5197. 

I've done this a couple of times and it was relatively simple. I never 
needed to use antechamber for anything else, all modelling and assignment 
of atom types were done manually. Exotic species might make things more 
complicated. 

P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For 
example, GROMOS FFs don't have a fixed recipe for obtaining the charges 
(you can even set them by hand according to your own whim), but the 
calculations must reproduce solvation enthalpies, etc. In sum, check the 
original literature on the FF you plan on using to understand how to 
calculate your own charges in a way that respects that specific FF's 
"philosophy". 

Hope it helps, 
João 



On Tue, Oct 3, 2017 at 3:16 PM, Sergio Manzetti < 
sergio.manzetti at fjordforsk.no> wrote: 

> Hi, I was wondering what the best approach is to simulate a negatively 
> charged topology imported from ANTECHAMBER (which can't do integral 
> charges): 
> 
> 1. Do QM calculations on the molecule, then edit the output from 
> Antechamber 
> 
> or 
> 
> 2. Do something else. 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ 
> | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ 
> http://www.phap.no/ | FAP ] 
> 
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