Hi InSuk,
Sorry I missed your original post. The reason sleap give the error message
is because your test.pdb has a slightly different format than usual pdbfile, i.e.
In your file there are line like this:
ATOM 451 O WAT A 18 4.314 0.826 1.622 1.00 0.00 O
^
while sleap is expecting:
ATOM 451 O WAT A 18 4.314 0.826 1.622 1.00 0.00 O
^
notice the different position of "O".
I will change to code of sleap so that it will accept this format. Meanwhile,
you can manually shift the position of "O" to left, so the current sleap will be
able to work.
Sincerely,
Wei
On Mar 25, 2010, at 1:10 PM, InSuk Joung wrote:
> I posted this while ago but I guess sleap developers missed this.
> Sleap developers, please see the problem below. Thanks!
>
> ---------- Forwarded message ----------
> From: InSuk Joung <i.joung.gmail.com>
> Date: Thu, Mar 4, 2010 at 5:55 PM
> Subject: sleap help
> To: amber.ambermd.org
>
>
> Hi,
>
> If I run with tleap, I don't have any problem.
> $ tleap -f leap.in
> ..
>
> With sleap, I get following errors.
> $ sleap -f leap.in
> ...
> Warning: there is an atom in residue WATA17 which does not exist in the
> model 3!
> This atom will not be created.
> Warning: there is an atom in residue WATA18 which does not exist in the
> model 3!
> This atom will not be created.
> Warning: there is an atom in residue WATA19 which does not exist in the
> model 3!
> This atom will not be created.
> Warning: there is an atom in residue WATA20 which does not exist in the
> model 3!
> This atom will not be created.
> Warning: there is an atom in residue WATA21 which does not exist in the
> model 3!
> This atom will not be created.
> Warning: there is an atom in residue WATA22 which does not exist in the
> model 3!
> This atom will not be created.
>
> Please try with the attached files.
>
> --
> Best,
> InSuk Joung
>
>
>
> --
> Best,
> InSuk Joung
> <leap.in><test.pdb>_______________________________________________
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Received on Thu Mar 25 2010 - 14:00:02 PDT
