Hi Collins,
I'm not sure I understand why you need to create an old prmtop file for it
to work. As far as I can tell from below you are trying to solvate the dna
unit before you have loaded anything that actually defines it. Hence Leap is
telling you that dna is not a unit, it is a string, i.e. just a word. If you
did the following:
source leaprc.ff99SB (or other force fields if you desire)
dna = loadpdb BDNA_15_GC.pdb
addions dna Na+ 0
solvateoct dna TIP3PBOX 10.0
saveamberparm dna BDNA_15_GC.prmtop BNDA_15_GC.inpcrd
This should work fine assuming your pdb is kosha and there are no errors
when you issue the dna=loadpdb command.
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Collins Nganou
Sent: Thursday, July 24, 2008 11:52 PM
To: amber.scripps.edu
Subject: AMBER: solvate dna in TIP3PBOX 10.0
Hi Ross,
I know this information about AMBER solvation. But it didn't walk.
> solvateoct dna TIP3PBOX 10.0
solvateOct: Argument #1 is type String must be of type: [unit]
usage: solvateOct <solute> <solvent> <buffer> [aniso] [closeness]
> solvateBox dna TIP3PBOX 10.0
solvateBox: Argument #1 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
But after running :
dna = loadpdb BDNA_15_GC.pdb
and set default Oldprmtopformat on
saveAmberParm dna BDNA_15_GC.atop BDNA_15_GC.rst
addions dna Na+ 0
Solvatebox dna TIP3PBOX 10.0
SaveAmberParm dna BDNA_15_GC.solv.atop BDNA_15_GC.solv.rst
After all this, I didn't have a problem.
But in this amber10, it is not possible to use this atop file.
Sander all time ask me to use a new top file prmtop.
But this Solvatebox dna TIP3PBOX 10.0 or solvateoct dna TIP3PBOX 10.0
didn't run.
I need it to run PB calculation
I don't know why?
This is my problem.
Thanks a lot for all response.
Collins
On Thu, Jul 24, 2008 at 2:29 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
Hi Collins,
In AMBER 9 and 10 WATBOX216 has been renamed as TIP3PBOX so you would
specify.
solvateoct dna TIP3PBOX 10.0
Good luck,
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Collins Nganou
Sent: Thursday, July 24, 2008 2:29 AM
To: amber.scripps.edu
Subject: AMBER: solvate dna in TIP3PBOX 10.0
Dear Amber,
I want to solvate dna in solvatebox TIP3PBOX 10.0, by:
> solvateOct dna WATBOX216 10
solvateOct: Argument #2 is type String must be of type: [unit]
usage: solvateOct <solute> <solvent> <buffer> [aniso] [closeness]
But this didn't work.
I use the set of parameters parmbsc0, describe in
http://mmb.pcb.ub.es/PARMBSC0/README.txt
Please someone can tell me how to process.
Thanks a lot.
Regards
Collins
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Received on Sun Jul 27 2008 - 06:07:43 PDT
