Peyman Yamin wrote:
On Monday 27 October 2008 18:08, Justin A. Lemkul wrote:
Peyman Yamin wrote:
Hi again dears,
I should ask for another comment. I have a Phorphorus to which two Oxygen
atoms are bonded. One O is double bonded and the other has only a single
bond while being negatively charged. In the topology file I get from
prodrg both Os are denoted with OA (GROMOS96.1) atom type. both have the
same charge (-0.421) and mass (15.9994). I guess the charge is reasonable
for the double-bonded one, but not for the one with a single bond and a
free electron. How could I correct this?
There is no true double or single bond. Think resonance!
Impressive answer! But, well, I'm not sure about that resonance thing?
...C-O-P(+3)-O-C... So far it's OK! but P still has 3 fellow electrons to
share. it does share two of them at once with another O. I understand till
here. there is another O who wants to get 2 electrons shared, but only
receives one: it needs more => so we call it a "negatively charges fellow
oxygen", don't we?
I think there are going to be two distinct atom types. For a few examples of
how to deal with phosphates, see the .rtp entry for ATP, or look at the lipids
that Peter Tieleman makes available online. If we consider a traditional Lewis
structure for the phosphodiester (hopefully this translates alright):
O
||
R--O--P--O--R
|
O-
Really the =O and --O^- are equivalent in terms of atom type (OM in Gromos) and
charge. The O in the phosphodiester linkages are likely to bear similar
charges, but have a different atom type (OE in Gromos). Hence why proper
parameterization takes a substantial amount of time.
Be careful if you're using the topology straight from PRODRG. Its
interpretation of charge groups and charges often requires a bit of refinement.
Also realize that Gromos96 is not the best for reproducing the properties of a
lipid, although I don't know if isolated lipids have been considered. The
Berger lipid parameters (Gromos/OPLS combination) are widely used...but that's a
whole other debate :)
Well I'm well aware of my chemistry knowledge fading away, but you'll tell me
an OA will do well for both??
Maybe for the phosphodiester O, but not for the =O and --O^-; they are more like
a carbonyl O (atom type OM).
-Justin
Thanks for the time, indeed,
Peyman
-Justin
Cheers,
Peyman
--
========================================
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
