Hello everyone,
I was wondering if someone could help me about the procedure of creating forcefield of glycine zwitterion for my case.
I am trying to find the GAFF(1st ver.) force field parameters for zwitterion glycine using tutorials (
http://ambermd.org/tutorials/basic/tutorial4b/).
I am trying to perform a clustering simulation of glycine in water and also organic solvent.
But I am not sure whether the following procedure is correct or not. Because I at least found that O-C-O angle is not equivalated to 130.25 (degree) even if it is in the diluted situation of glycine water solution.
Based on “Crystal Growth & Design, Vol. 10, No. 12, 2010” and “CrystEngComm,2017, 19, 7197”, the GAFF+CNDO combination is known as suitable for crystallization/clustering of glycine molecule in water.
I have only the tool of antechamber, no other DFT tool/software.
My current procedure is as follows.
1. Read “PDB file (zwitterion glycine)”
HETATM 1 N01 gly 1 -1.074 -0.432 -0.006 0.021000
HETATM 2 H01 gly 1 -1.471 -1.367 -0.015 0.190000
HETATM 3 H02 gly 1 -1.384 0.104 -0.824 0.190000
HETATM 4 H03 gly 1 -1.385 0.090 0.821 0.190000
HETATM 5 C01 gly 1 0.409 -0.432 -0.006 -0.021000
HETATM 6 H04 gly 1 0.774 -0.942 -0.934 0.031500
HETATM 7 H05 gly 1 0.785 -0.970 0.899 0.031500
HETATM 8 C02 gly 1 0.967 1.067 -0.006 0.375000
HETATM 9 O01 gly 1 0.074 1.950 -0.022 -0.504000
HETATM 10 O02 gly 1 2.204 1.149 0.007 -0.504000
1. Get mol2 file with using AM1-BCC charge
2. Parameter check -> create frcmod.
3. Replace directly from AM1-BCC to CNDO (initial value in PDB file above) for each atom in text editor
4. Assign the GAFF parameter and prmtop
Maybe, the direct rewriting of the charge is not right procedure.
But I need to use these values which already showed the validity of crystallization of glycine molecule in the water. I could not find in the past questions for this situation.
Could someone help guide me for this issue?
Best regards,
Akira Kitayama, PhD candidate in science and engineering, Doshisha univ., Kyoto
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Received on Sun Nov 11 2018 - 08:30:02 PST
