On 2012-01-12 12:42, g...@bioacademy.gr wrote:
Hi
Many thanks for your reply and sorry to come back on this.
Is the fitting to experimental free energies of solvation, the
only acceptable way to get "GROMOS-compatible charges"? Acceptable
because this is the way that partial charges were derived for the
gromos ff.
In the quite usual case that these experimental data are not available
for the ligand one is interested in, are DFT/ESP charges acceptable?
No. CHeck http://compbio.biosci.uq.edu.au/atb/
Thanks again.
George
g...@bioacademy.gr wrote:
Hello
Given that the partial charges from PRODRG are not reliable (as
explained
Justin Lemkul's paper),
are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable
starting point?
Yes, those charges are a reasonable start, but will almost certainly not
be
sufficient for the final topology.
In this case, do we treat all ligand atoms as one charge group?
Unless your ligand is 4 atoms or less, no. Please consult the manual
regarding
charge groups, and see existing Gromos96 building blocks for suitable
charge
groupings.
-Justin
--
========================================
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
========================================
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