AMBER Archive (2008)

Subject: Re: AMBER: solvate dna in TIP3PBOX 10.0

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sat Jul 26 2008 - 13:11:44 CDT

> Hi Bill
>
> I create it by dna = loadpdb BDNA_15_GC.pdb
>
> Then I add Na+ by
>
> addions dna Na+ 0
>
>
> But solvateBox dna TIP3PBOX 10.0 didn't run, I didn't know why?

This is a mystery. Try 'list' to see all defined units and make sure that
'dna' and 'TIP3PBOX' both appear. If they do, and if you still get the error
message, I think it is a matter for the developers to try to reproduce and
debug.

Bill

>
>
> Regards
>
> On Fri, Jul 25, 2008 at 10:28 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:
>
> > > > solvateBox dna TIP3PBOX 10.0
> > > solvateBox: Argument #1 is type String must be of type: [unit]
> >
> > 'dna' is argumet #1 - how did you create it?
> >
> > E.g.
> >
> > > dna = loadpdb mydna.pdb
> >
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