From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Mon Sep 03 2007 - 10:47:35 CDT
Hi,
Indeed there are some special issues for simulating heavy metals. The
fact is that some properties of the metal fail to be mimicked by the
simplification assumed in classical molecular dynamics, i.e. describing
the metal with just charge and L-J parameters. Just to mention one
example, the geometry of the coordination site is lost when performing
simulations for some metals like Cu or Zn. There are several
publications that suggest how to deal with those systems. For the
citations of these papers you can start by doing a search on namd and
charmm forums.
Regards
Cesar
Deepangi Pandit escribió:
> Hello:
> Well, my progress is slow but it seems there are two issues Topology
> and Parameters. I am listing my understanding below. Please correct me
> if I am wrong. I am editing topology and parameter files for the first
> time.
>
> Based on replies of Purushottam, Harish and jfgaff_at_ncsu.edu, I
> performed following editions.
>
> TOPOLOGY
>
> I edited the topology file to include Copper and sulphate ions. Zinc
> is already available in top_all27_prot_lipid.inp so as mentioned by
> Harish, I will just have to read it in a separate segment and change
> ZN in PDB to ZN2, CU2 for CU. Please find topology of sulphate anion
> based on methylsulphate and Cu ion based on Zn ion. Does it look OK?
>
> MASS 93 CU 63.54600 CU ! copper(II) cation
>
> RESI CU2 2.00 ! Copper ion
> GROUP
> ATOM CU CU 2.00
> PATCHING FIRST NONE LAST NONE
>
> RESI SO4 -2.00 ! sulfate anion
> GROUP !
> ATOM S SL 1.33 ! OS2(-1)
> ATOM OS1 OSL -0.28 ! |
> ATOM OS2 O2L -0.65 ! (-1) OS3--S(+2)--OS4 (-1)
> ATOM OS3 O2L -0.65 ! |
> ATOM OS4 O2L -0.65 ! OS1(-1)
> !
> BOND S OS1 S OS2 S OS3 S OS4
> ACCE OS1
> ACCE OS2
> ACCE OS3
> ACCE OS4
>
> IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000
> IC OS2 S OS2 OS3 0.0000 0.0000 -60.0000 0.0000 0.0000
> IC OS3 S OS1 OS4 0.0000 0.0000 60.0000 0.0000 0.0000
> IC OS1 S OS3 OS2 0.0000 0.0000 60.0000 0.0000 0.0000
> IC OS1 S OS4 OS2 0.0000 0.0000 180.0000 0.0000 0.0000
> IC OS1 S OS2 OS3 0.0000 0.0000 180.0000 0.0000 0.0000
> IC OS1 S OS3 OS2 0.0000 0.0000 180.0000 0.0000 0.0000
> IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000
> IC OS4 S OS3 OS1 0.0000 0.0000 60.0000 0.0000 0.0000
> IC OS3 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000
>
> PARAMETER
>
> I think I can use ZN parameters for CU as they are close. Am I right?
> So I plan to add the following to the parameter file
>
> CU 0.000000 -0.250000 1.090000 ! ALLOW ION
>
> For sulphate ion I plan to use O2L and SL parameters. Is it Ok to do that?
>
> O2L 0.0 -0.12 1.70
> SL 0.0 -0.47 2.1
>
> Other details:
>
> Zn and Cu are bonded to Histidines.
>
> I am sharing file changes to the list members as I want to make sure I
> am on the right path.
>
> Thank you,
> Deepangi
>
>
>
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