[gmx-users] R: Re: adding a new residue in the ff

[Anna Marabotti]

Dear Justin and Tsjerk,
thank you very much for your last encouraging words...;-) I don't remember a
time in my life where something that I needed, which was very complex to do,
was already available...(apart from Gromacs package, of course!)
About parameterization: sure I was intended to use the parameters for Cys
residue as much as possible. I was thinking of adding all angles, bonds,
dihedrals etc until the CB, and using the topology created by PRODRG only
for SO3 moiety. If I understand well, Tsjerk suggests not to include the
CA-CB-SG angle. Concerning charges, I was planning to calculate them using
Antechamber, following Justin's suggestions about the problems of Prodrg.
IIRC, apart from charges, bonds, angles, dihedrals etc. obtained with Prodrg
were substantially correct, so I was thinking of adding directly these
values to my ffbonded.itp. The atom types of SO3 seem to be already present
in the ffG43a1, since they are identified as SDSMO and OM. Do you think that
with these data I would be able to add the bonds, angles etc to my
ffbonded.itp, to aminoacids.rtp and all other files I have to modify in the
ffG43a1 local forcefield? I don't think to be able to obtain an "exact"
parameterization, but I hope it would be at least acceptable...
Many thanks 
Anna


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Message: 1
Date: Thu, 31 Mar 2011 19:27:17 +0200
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] adding a new residue in the ff
To: jalemkul at vt.edu, Discussion list for GROMACS users
	<gmx-users at gromacs.org>
Message-ID:
	<AANLkTikae2L6DdpFsZjJXXLqEkLxWGd1HETWSkeMvv53 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi,

> It would probably be easier, faster, and more accurate to just use most of
> the parameters for Cys rather than try to have PRODRG re-create a
> (potentially flawed) model of your compound.  The only new parameters are
> related to SO3, so the rest should be identical to the Cys residue.

That's not a good idea. It'll only do for the backbone. The charge of
CB will be quite different, as well as the CA-CB-SG angle, and for the
rest there's nothing similar even.

> This is where parameterization becomes a chore - when there's nothing
> analogous to what you're doing.  Proper Gromos96 parameterization
> methodology would dictate that you generate an analogous compound (i.e.,
> methyl sulfonic acid) and adjust its parameters such that it reproduces
> various condensed-phase thermodynamic and physical properties (DeltaG of
> solvation, liquid density, heat of vaporization).  Proper derivation is
> quite time-consuming.  Perhaps someone has already done this work and it
is
> published.  If you're unlucky, you've got to do it all yourself.

That's a good idea :)

Cheers,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands


------------------------------

Message: 2
Date: Thu, 31 Mar 2011 13:29:54 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] adding a new residue in the ff
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Message-ID: <4D94BA12.5030701 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Tsjerk Wassenaar wrote:
> Hi,
> 
>> It would probably be easier, faster, and more accurate to just use most
of
>> the parameters for Cys rather than try to have PRODRG re-create a
>> (potentially flawed) model of your compound.  The only new parameters are
>> related to SO3, so the rest should be identical to the Cys residue.
> 
> That's not a good idea. It'll only do for the backbone. The charge of
> CB will be quite different, as well as the CA-CB-SG angle, and for the
> rest there's nothing similar even.
> 

Gah, that's what I meant.  Thanks for pointing that out!  I guess I've
stated so 
many times (and published on the fact) that PRODRG charges are useless that
I'm 
no longer even quoting myself...

-Justin

>> This is where parameterization becomes a chore - when there's nothing
>> analogous to what you're doing.  Proper Gromos96 parameterization
>> methodology would dictate that you generate an analogous compound (i.e.,
>> methyl sulfonic acid) and adjust its parameters such that it reproduces
>> various condensed-phase thermodynamic and physical properties (DeltaG of
>> solvation, liquid density, heat of vaporization).  Proper derivation is
>> quite time-consuming.  Perhaps someone has already done this work and it
is
>> published.  If you're unlucky, you've got to do it all yourself.
> 
> That's a good idea :)
> 
> Cheers,
> 
> Tsjerk
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================