Anna Marabotti wrote:
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.
Results from Antechamber directly are probably not sufficient as an end state
for parameterization. See our recent paper about this:
http://pubs.acs.org/doi/abs/10.1021/ci100335w. Antechamber gives you a
reasonable starting point, but the calculations do not even replicate the most
trivial species in the Gromos96 43A1 parameter set (nor would you necessarily
expect them to).
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
If they're "correct," then what do you need to add? If they are already part of
the parent force field (i.e., PRODRG chose correct values) then you do not need
to re-define existing parameters (and in fact, grompp may raise a fatal error if
you do).
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...
Your desired level of accuracy is up to you, but most careful reviewers do not
consider partial efforts to be sufficient. Close enough is not necessarily good
enough. The approximations or substitutions you make need to be justifiable,
which I guess is about as good as anyone can recommend.
-Justin
Many thanks
Anna
----------------------------------------------------------------------
Message: 1
Date: Thu, 31 Mar 2011 19:27:17 +0200
From: Tsjerk Wassenaar <tsje...@gmail.com>
Subject: Re: [gmx-users] adding a new residue in the ff
To: jalem...@vt.edu, Discussion list for GROMACS users
<gmx-users@gromacs.org>
Message-ID:
<aanlktikae2l6ddpfszjjxxlqeklxwgd1hetwskemv...@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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
