Dear Amber-Team,
I am greatfully using the MCPB.py tool to create .itp files for my
GROMACS simulations of organometallic API in different solvents to
determine the solvation free energy. I have two different types of
molecule as shown in the pictures below. Up till now, I am using the
RESP method to determine the charges as performed with Step 3a of the
MCPB.py script.
Now, I would like to use AM1-BCC or ABCG2 charges for the organic part
of the molecules and I start reading into the options. I already found
out that I could use antechamber to convert the RES.pdb to RES.mol2 with
bcc charge calculation. At this point there are some questions raising:
1) My RES.pdb for AuSingle contains der NHC ring and the chlorid so
there is a hole when the Au is seperated. Is it still feasable to use
this option for my kind of molecules?
2) I had to give the RES an organic charge. I tried 0 and -0.25
(according to the Mulliken charges) but the calculation stops. Just -1
is an acceptable input and this creates charges for Au with +2.5 and
+4.45 for c in the methyl rest. How do I chose the organic charge?
3) I tried different ChgMod Options A, B and C for Step 3 of MCPB.py but
I always this alsways results in the same charges. I hope that you are
willing to explain which part of the charge calculation is covered by
AM1-BCC and what is being done in step 3. Do you have recommendation for
my molecules? And even more important: is it consistant to use AM1-BCC
charges for the organic "part" and RESP charges for the Au since
AuSingle is a bonded molecule with Au in the middle?
4) I tried to use AM1-BCC and ABCG2 as semi-empirical charge methods.
The different lays in the parameter file
~/amber20/dat/antechamber/BCCPARM. For my organic solvent I successfully
applied ABCG2 charges when I used antechamber to extract the
octanol.mol2 and octanol.prep from the gaussian output. But when I used
ABCG2 for the organometallic complex to convert RES.psb to RES.mol2, I
received the same charges in the end. I have the feeling that my the bcc
charge calculation is not performed correctly and I am struggeling to
find the solution.
I would be very greatful to hear from you and I hope you can give my
some usefull advises.
Have a nice day and kind regards
Miriam Sprick
(In the AUSINGLE.zip folder I attached my input files. In case the 15 MB
folder is send incorretly, please let me know!)
AuDouble:R=CH3
AuSingle: R = CH3
--
M.Sc. Miriam Sprick (she/her)
Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany
Tel: +49 (0)531 391-2634
https://www.tu-braunschweig.de/ift/agmolth
https://www.tu-braunschweig.de/pvz/projekte/drugdiscovery
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Received on Wed Feb 14 2024 - 04:00:03 PST
