Nagy, Peter I. wrote:
Dear Tom,
I read your e-mail in the gmx-users mailing list, and decided to
answer in a personal mail.
(I am not eager to appear on that list...)
Why that?
In my opinion, your approach is basically correct. It is a matter
of consideration whether the
RHF/6-31G* level for geometry oprimization is correct. Generally, for
a POSITIVELY charged
closed shell system RHF/6-31G* may be acceptable. If the ion is
negatively charged, consideration of diffuse functions are needed.
What I normally do, I perform the optimization
with both basis sets, and see if the geometry differs.
The next problem: do you want to study your molecule in the gas
phase of in solution? The HF/6-31G* optimization and charge derivation
was suggested by the Jorgensen group, because the dipole moment at
this level (optimization performed in the gas-phase) is exaggareted by
about 20% and this overestimation accounts for some polarization
appearing in solution. Thus this calculation may provide acceptable
charges for in-water calculations, but probably not for gas-phase or
in non-polar solution.
I noticed that you created the CHELPG ELPO map, and then
recalculated the charges with a
RESP fit. I assume that the CHELPG and the RESP charges differ quite
remarkably. My recent
experience is that the CHELPG charges provide too polar charge
distribution, and the RESP
charges derived in this way may serve better. But if the two sets,
CHELPG and RESP differ
too much, you would need an independent verification of the preference.
I am interested in this problem, and if you want you may write me in
a personal e-mail. We can
further discuss the problem, and I could say more if having some idea
about your system. Also,
B3LYP/6-31G* optimization may be an alternative and/or optimization in
solution using the IEF-PCM method. This may be discussed if you want
to continue this correspondence.
Best regards
Peter I. Nagy
The University of Toledo
Toledo, OH, 43606, USA
------------------------------------------------------------------------
*From:* [EMAIL PROTECTED] on behalf of TJ Piggot
*Sent:* Wed 8/30/2006 8:21 AM
*To:* gmx-users@gromacs.org
*Subject:* [gmx-users] OPLS-AA Charge Calculation
Hi all,
I am trying to calculate partial charges of a ligand for the OPLS-AA/L
forcefield. I have searched the mailing lists and literature and would
like
to confirm that the approach i am going to take is a sensible and accurate
one.
Firstly i take an all atom structure of the ligand and minimise in
gaussian03 using the RHF method and 6-31G* basis set (is this a suitable
level of theory for my charged ligand of 43 atoms?).
Then i calculate the electrostatic potential using the CHelpG method and
output it on a grid.
Then use a two stage RESP fitting to calculate the charges.
Thanks for any input you have on this approach
Tom Piggot
----------------------
TJ Piggot
[EMAIL PROTECTED]
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
