AMBER Archive (2007)

Subject: AMBER: ADDIONS do not neutralize to ZERO

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Mon Jan 22 2007 - 19:19:20 CST

Dear Amberites

I am trying to simulate a membrane protein for which I tried to add
ions using the "addions2" command of the TLEAP using Amber9

In my system, the ligand has a formal negative charge (-1)

I get the following error when I add ions

--------------------------------------------------------------------------------------------------------------
> addions2 ang Cl- 0
14 Cl- ions required to neutralize.
Adding 14 counter ions to "ang" using 1A grid
Total solute charge: 14.97 Max atom radius: 2.10
Grid extends from solute vdw + 2.47 to 8.57
Box:
   enclosing: -21.55 -14.01 -9.56 127.85 115.23 81.21
   sized: 234.45 241.99 246.44
   edge: 256.00
Resolution: 1.00 Angstrom.
Tree depth: 8
grid build: 9 sec
Volume = 1.92% of box, grid points 321630
Calculating grid charges
charges: 9450 sec
Placed Cl- in ang at (63.45, 54.99, 50.44).
Placed Cl- in ang at (38.45, 49.99, 73.44).
Placed Cl- in ang at (36.45, 75.99, 48.44).
Placed Cl- in ang at (9.45, 43.99, 52.44).
Placed Cl- in ang at (62.45, 53.99, 23.44).
Placed Cl- in ang at (31.45, 49.99, 44.44).
Placed Cl- in ang at (46.45, 63.99, 73.44).
Placed Cl- in ang at (48.45, 100.99, 16.44).
Placed Cl- in ang at (58.45, 30.99, 26.44).
Placed Cl- in ang at (64.45, 69.99, 56.44).
Placed Cl- in ang at (49.45, 84.99, 74.44).
Placed Cl- in ang at (22.45, -2.01, 3.44).
Placed Cl- in ang at (62.45, 21.99, 74.44).
Placed Cl- in ang at (32.45, 66.99, 74.44).

Done adding ions.
> saveamberparm ang angitelmi_DMPC_ions_initial.prmtop angitelmi_DMPC_ions_initial.inpcrd
Checking Unit.
ERROR: The unperturbed charge of the unit: 0.970410 is not integral.
WARNING: The unperturbed charge of the unit: 0.970410 is not zero.
--------------------------------------------------------------------------------------------------------------

I defined in my command to neutralize the system until the charge
becomes '0'. Can you suggest me what is going wrong, or if it is
okay??

Best Regards
Akshay (Olemiss)

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Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17_at_olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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