Hi!
Thanks for your reply.
I obtained the file jac_box.prmtop by typing on sleap the following:
set default echo on
source leaprc.amoeba
test = loadpdb jac_2.pdb
solvatebox test WATBOX 4.0
savepdb test jac_box.pdb
saveamoebaparm test jac_box.prmtop jac_box.xyz
quit
Then I used these files (prmtop and xyz) as input to run sander.
Thank you,
Susana
Hi,
How did you get the file jac_box.prmtop? since it is not
originally in the directory?
There is a hpv.prmtop.save which contain solvent box. you might want
to try that one.
Sincerely,
Wei
On Apr 7, 2009, at 11:34 AM, Tomasio, Susana wrote:
>
>
> Sorry.. it is on amber10/test/sleap/amoeba.
>
> After building and solvating the box and saving the .prmtop and .xyz
> files I tried to run:
>
> /home/msrgah/amber10/exe/sander -O -i midin -o test.out -p
> jac_box.prmtop -c jac_box.xyz -r jac_.rst
>
> And I got that error.
>
> Thanks,
>
> Susana
>
>
>
>
>
>
>
>
> -----Original Message-----
> From: amber-bounces.ambermd.org on behalf of David A. Case
> Sent: Tue 4/7/2009 5:29 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] test/amoeba - forrtl: severe (64): input
> conversion error
>
> On Tue, Apr 07, 2009, Tomasio, Susana wrote:
>>
>> I'm having a problem in running the example on amber10/test/amoeba/.
>
> As far as I can see(?), there is no such directory. Can you report
> *exactly* what commands you ran (rather than just say "when I try to
> run
> sander....")
>
> ...dac
>
>
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Received on Wed Apr 08 2009 - 01:19:34 PDT
