Hello Changwoon,
You can check the performance of the gaff parameters for both of these molecules using Wolf2Pack. For furan, there are 347 QM data points for 16 internal coordinates available for comparison. Similarly, for thiopene there are 349 QM data points for 16 internal coordinates. The QM data points include HF/6-31G(d) constrained optimized geometries and MP2/aug-cc-pVDZ//HF/6-31G(d) single-point energies. The internal coordinates represent all symmetry equivalent internal coordinates of the molecules. To check the default gaff parameters, you can simply take the output of parmchk and copy-paste it into the force field section of the "MM Constraint Optimization" page of Wolf2Pack.
You will see that several parameters perform well, but there are some that require optimization for better agreement to the QM data.
You will also find the partial atomic charges for each molecule as computed by R.E.D. These charges are compatible for use with the parm99SB force field (i.e. the protein force field).
Cheers,
Karl
(www.wolf2pack.com)
----- Original Message -----
From: "Chang Woon Jang" <changwoonjang.yahoo.com>
To: amber.ambermd.org
Sent: Monday, April 22, 2013 4:17:00 PM
Subject: [AMBER] dihedral term for furan and thiophene molecules
Dear Amber Users,
I am trying to find the general amber force field (gaff) dihedral parameters for furan and thiophene molecules.
In the gaff.dat, there are no "cc-os-cc-cd" and "cc-ss-cc-cd" type parameters in the dihedral term.
cc - Sp2 carbons in non-pure aromatic systems
os - Ether and ester oxygen
cd - Sp2 carbons in non-pure aromatic systems, identical to cc
ss - Sp3 S in thio-ester and thio-ether
I have searched few papers and old amber ffs, but I could not find them for gaff.
If you know these type parameters, would you please let me know or how can I find them?
Thanks.
Best regards,
Changwoon Jang
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Received on Tue Apr 23 2013 - 05:00:02 PDT
