AMBER Archive (2008)

Subject: RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 15 2008 - 10:50:20 CDT

Hi Grange,

 

My point is that even though the CHU and CHV are covalently connected
doesn't mean you should refit the entire thing, you just want to cap these
units and fit the charges for them on their own. The standard amino acids
you should leave as the RESP charges from the FF99SB force field, along with
their parameters.

 

Note, "a complete force field" does not mean a perfect force field, with
more generality obviously comes more approximation. Hence what you are doing
here is increasing the "error" for the parameters for the standard amino
acids in order to obtain parameters for your non-standard residues. This is
probably not the best way to go about it. As a first pass you should
probably keep all the standard residues as FF99SB and just use GAFF for the
CHU and CHV residues. Of course since they are covalently bound you will
have to deal with capping groups. There is an example of this here:
http://amber.scripps.edu/antechamber/pro4.html although I have never worked
through this tutorial myself to check it all works correctly but it should
help you out.

 

The other approach as I suggested is to cap the CHU and CHV residues, do a
HF/6-31G* full RESP fit to get charges then try to select atom types based
on the existing amino acid templates. Anything that is missing you will have
to generate your own parameters for.

 

All the best

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Grange Hermitage
Sent: Monday, July 14, 2008 12:42 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop

 

Thanks, Ross.

The CHU and CHV are covalently connected.
I tried defining this using gromacs rtp entries in ffG43a2 and OPLS, both
based on serine and taking all defaults, but the systems produced are
unstable.

The advice being reinforced by my experiences there is that when extending a
force field you must go back to methods originally used to define the force
field. I am using GAFF because it is a complete force field.

On Mon, Jul 14, 2008 at 2:05 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

 

 In fact in your case your system comprises a number of individual residues
so you probably shouldn't be using antechamber at all and it is not clear to
me why you want to do it this way. Except for the CHU, AIB and CHV
everything looks to be standard residues

 

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