Hi Lizelle,
The third column is polarizability, it is not used in non-polarizable force field simulation.
Kind regards,
Pengfei
> On Aug 31, 2017, at 5:03 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
>
> 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:
>
> MASS
> 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
> Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via csirt.uct.ac.za
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 31 2017 - 08:00:03 PDT
