nahren manuel wrote:
Dear Gromacs USERs,
My ligand, which contains a piperazine ring & needs to be positively
charged (+1).
When I assign Gasteiger charges, it comes out to be -0.336 on the
Nitrogen.
But When I do a SEMI-EMPIRICAL PM3 to place my partial charge , it
puts +0.733 on this atom. So does it mean it has put partial charge as
(F.Charge - P. Charge). When I use InsightII (cff91 FF), the partial
charge on this ligand was -0.556 and also it had a formal charge of
+1. So kindly suggest me the best way out.
The "best way out" is the one that you believe to be most defensible for
your particular situation. I would suggest looking up some of the
original references for force field derivations (OPLS, GROMOS, AMBER,
etc.) to get a sense of what types of methods are typically employed in
deriving parameters. If you can find similar functional groups that
have already been parameterized, that would probably be a good resource.
Also, does gromacs takes formal charges automatically or is there a
way to define the same.
Gromacs will assign charges to each atom based on what you provide in
the .itp file.
-Justin
thanks
nahren
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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 [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
