AMBER Archive (2008)

Subject: AMBER: solvate dna in TIP3PBOX 10.0

From: Collins Nganou (nganoucollins_at_gmail.com)
Date: Fri Jul 25 2008 - 01:51:54 CDT

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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