[AMBER] frcmod file format

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Thu, 31 Aug 2017 10:03:45 +0000

Hi All,

I have created an frcmod file for the coordination of 4 ligands (Glutamate, Histidine, Histidine and water) to Zn.
The first part is as follows:

X1 14.01 0.530 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
X2 14.01 0.530 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
X3 16.00 0.434 carboxyl and phosphate group oxygen
X4 16.00 0.000 oxygen in TIP3P water
Z1 65.4 Zn ion

I understand that column 2 gives the mass of each atom but can someone please explain to me what the third column is?
Is it strange that the value for oxygen in water is 0.000 while in glutamate (X3) it is not? Also, is a value needed for the Zn ion?

Kind regards

Lizelle Lubbe

PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Thu Aug 31 2017 - 03:30:02 PDT
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