AMBER Archive (2008)

Subject: RE: AMBER: solvate dna in TIP3PBOX 10.0

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jul 25 2008 - 03:14:26 CDT

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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Collins Nganou
Sent: Thursday, July 24, 2008 11:52 PM
To: amber_at_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_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Collins Nganou
Sent: Thursday, July 24, 2008 2:29 AM
To: amber_at_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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