AMBER Archive (2002)

Subject: Question about Counterions

From: Markus Drumm (mdrumm_at_biomedicale.univ-paris5.fr)
Date: Thu Sep 19 2002 - 12:38:24 CDT

Dear Amber Users,

I'm trying to use the old fashioned prep/link/edit/parm methodology to
create a protein molecule in a solvent box. I 've done this frequently
for DNA by going twice through link/edit/parm and addeing first the
counterions and then the solvent box.
When trying to this with my protein, edit doesn't add any counterions to
my system, although I tried a lot of CMIN SDIST DISCK CUTSB values.
So I switched to leap which adds nicley 12 counterions. When I try to
solvate my system, leap (Amber6 package) fails to create a proper
top.file. I wanted to use the pdb file with the counterions created by
leap before which looks fine. Below, I post the .pdbin with the
counterions and my .linkin. The third file ist the counterion-part of
the .linkout which obviously looks strange in the sense, that link fails
to convert the Z-matrix values into cartesian coordinates. Anyway, I
don't get any error message in .linkout.
So, if anybody has encountered the same problem or knows how to deal
with it, I would appreciate any suggestions.
Thanks very much,

Markus Drumm.

***** File.pdbin*****
TER
ATOM 1486 Cl- CIM 87 -5.452 -2.695 -4.851
TER
ATOM 1487 Cl- CIM 88 3.548 -6.695 -2.851
TER
ATOM 1488 Cl- CIM 89 1.548 -9.695 6.149
TER
ATOM 1489 Cl- CIM 90 -4.452 -13.695 -1.851
TER
ATOM 1490 Cl- CIM 91 6.548 8.305 -2.851
TER
ATOM 1491 Cl- CIM 92 12.548 -13.695 -3.851
TER
ATOM 1492 Cl- CIM 93 -1.452 -2.695 13.149
TER
ATOM 1493 Cl- CIM 94 2.548 -1.695 -7.851
TER
ATOM 1494 Cl- CIM 95 7.548 1.305 -9.851
TER
ATOM 1495 Cl- CIM 96 -2.452 -5.695 7.149
TER
ATOM 1496 Cl- CIM 97 -6.452 -6.695 3.149
TER
ATOM 1497 Cl- CIM 98 -10.452 -6.695 -0.851
TER

*****file.linkin******

Chloride counterions
O 0 1 3 0
CIM 2*** CIM 2*** CIM 2*** CIM 2*** CIM 2*** CIM 2***
CIM 2*** CIM 2*** CIM 2*** CIM 2*** CIM 2*** CIM 2***

*****file.pdbout******

ATOM 1484 CL- CIM 87 15.000 90.000 180.000 -1.000
ATOM 1485 CL- CIM 88 1.000 90.000 179.985 -1.000
ATOM 1486 CL- CIM 89 1.000 90.000 179.996 -1.000
ATOM 1487 CL- CIM 90 1.000 90.000 180.000 -1.000
ATOM 1488 CL- CIM 91 1.000 90.000 180.000 -1.000
ATOM 1489 CL- CIM 92 1.000 90.000 180.000 -1.000
ATOM 1490 CL- CIM 93 1.000 90.000 180.000 -1.000
ATOM 1491 CL- CIM 94 1.000 90.000 180.000 -1.000
ATOM 1492 CL- CIM 95 1.000 90.000 180.000 -1.000
ATOM 1493 CL- CIM 96 1.000 90.000 180.000 -1.000
ATOM 1494 CL- CIM 97 1.000 90.000 180.000 -1.000
ATOM 1495 CL- CIM 98 1.000 90.000 180.000 -1.000 

-- 
********************************************************************************
Dr. Markus Drumm
Postdoctoral Research Fellow
Equipe de Chimie Bioinorganique et de Modelisation Moleculaire
CNRS UMR 8601
45, Rue des Saints-Peres
75270 Paris Cedex 06
France
********************************************************************************