From: Deepangi Pandit (dnp5_at_njit.edu)
Date: Fri Aug 24 2007 - 15:27:47 CDT
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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