Many thanks, Daniel,
Bingo. ambpdb works a treat. It must be a problem with saveMol2 under leap.
I'm on AmberTools 12, patch level 35 (fully up to date)
Thank you!
Regards,
John
==== === == = = = = = = = = = =
John Gehman Office +61 3 8344 2417
ARC Future Fellow Fax +61 3 9347 8189
School of Chemistry Magnets +61 3 8344 2470
Bio21 Institute Mobile +61 407 536 585
30 Flemington Rd jgehman.unimelb.edu.au
Univ. of Melbourne .GehmanLab
VIC 3010 Australia
http://www2.chemistry.unimelb.edu.au/staff/jgehman/research/
"Crooked nails hold better" (JDG, unpublished data)
==== === == = = = = = = = = = =
From: Daniel Roe <daniel.r.roe.gmail.com<mailto:daniel.r.roe.gmail.com>>
Reply-To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Date: Thursday, 21 March 2013 1:40 AM
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: Re: [AMBER] solvating and neutralizing a lipid bilayer
Hi,
What version of AmberTools are you using? Also, when you visualize the
resulting topology/restart files, do they appear to have the same
connectivity problems? I don't often use the savemol2 functionality of
tleap so it is possible something strange is happening there. I would
suggest if you require a mol2 file to either use ambpdb with the
'-mol2' flag or cpptraj to convert from topology/restart to mol2.
-Dan
On Wed, Mar 20, 2013 at 8:16 AM, John Gehman <jgehman.unimelb.edu.au<mailto:jgehman.unimelb.edu.au>> wrote:
Hello All,
I'm attempting to create a lipid bilayer, but I am running into problems with the solvation and neutralisation. The bilayer normal is parallel to y (an artefact left over from my having built it in Chimera) in the LEaP script copied below. If I add the correct number of Na+ to neutralise BEFORE solvating, the Na+ ions that wind up around the perimeter of the acyl chains get treated like solute, and I get a layer of water around this perimeter, too, upon solvating.
If, instead, I solvate FIRST, then addIons (or addIons2), as near as I can tell, the oxygens get deleted where steric clashes occur, but NOT their respective hydrogens. Inspection of the resulting mol2 file looks like spirograph gone mad in the water region, with lots of zigzags connecting Na+ atoms to far flung coordinates somewhere, too. This is presumably due to the connectivity problems after re-indexing the serial numbers for Na+ vs the original oxygen serial numbers.
Is this a bug, or have I done something daft? "Daft" is entirely possible — I had a week's introduction to AMBER ~two years ago, on a simple peptide, and I'm only just getting back into it. I've combed the manuals and archives, but couldn't find anything that made the difference.
Many thanks for your help,
John
logFile tleapPCL80.log
source leaprc.ff99SB
source leaprc.lipid11
loadOff PCL.lib
PCL80 = loadPdb "PCL80init.pdb"
solvatebox PCL80 TIP3PBOX {0.0 20.0 0.0} 1.0
addIons PCL80 Na+ 160
saveAmberParm PCL80 PCL80.prmtop PCL80.inpcrd
saveMol2 PCL80 PCL80.mol2 1
quit
==== === == = = = = = = = = = =
John Gehman Office +61 3 8344 2417
ARC Future Fellow Fax +61 3 9347 8189
School of Chemistry Magnets +61 3 8344 2470
Bio21 Institute Mobile +61 407 536 585
30 Flemington Rd jgehman.unimelb.edu.au<mailto:jgehman.unimelb.edu.au>
Univ. of Melbourne .GehmanLab
VIC 3010 Australia
http://www2.chemistry.unimelb.edu.au/staff/jgehman/research/
"Science really suffers from bureaucracy. If we hadn't broken
every single WHO rule many times over, we would never
have defeated smallpox. Never."
-- Isao Arita, final director of the WHO smallpox eradication program
==== === == = = = = = = = = = =
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto:AMBER.ambermd.org>
http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto: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 Wed Mar 20 2013 - 09:00:04 PDT
