--- On Mon, 12/1/08, oguz gurbulak <gurbulakoguz.yahoo.com> wrote:
From: oguz gurbulak <gurbulakoguz.yahoo.com>
Subject: Fw: Re: AMBER: using packmol file in Amber
To: "oguz gurbulak" <gurbulakoguz.gmail.com>
Date: Monday, December 1, 2008, 2:28 PM
--- On Mon, 12/1/08, oguz gurbulak <gurbulakoguz.yahoo.com> wrote:
From: oguz gurbulak <gurbulakoguz.yahoo.com>
Subject: Fw: Re: AMBER: using packmol file in Amber
To: amber.scripps.edu
Date: Monday, December 1, 2008, 1:18 PM
--- On Mon, 12/1/08, oguz gurbulak <gurbulakoguz.yahoo.com> wrote:
From: oguz gurbulak <gurbulakoguz.yahoo.com>
Subject: Re: AMBER: using packmol file in Amber
To: amber.scripps.edu
Date: Monday, December 1, 2008, 10:23 AM
check OAS
FATAL: Atom .R< HEP 1>.A<C1 1> does not have a type.
FATAL: Atom .R< HEP 1>.A<C2 2> does not have a type.
.
.
Warning: Close contact of 1.936478 angstroms between .R< HEP 5> .A<C7 7>
and R< HEP 5> .A<H15 215>
Warning: Close contact of 1.535878 angstroms between .R< HEP 5> .A<C7 7>
and R< HEP 5> .A<H16 228>
saveamberparams OAS h.prmtop h.inpcrd ( leap create EMPTY input files )
I attached the packmol file to mail. Could you please examine this file and tell me the reason of all these FATALS and Warnings? What should I do in order to load this packmol file succesfully into leap?
Thanks in advance.
--- On Tue, 11/25/08, David A. Case <case.biomaps.rutgers.edu> wrote:
From: David A. Case <case.biomaps.rutgers.edu>
Subject: Re: AMBER: using packmol file in Amber
To: amber.scripps.edu
Date: Tuesday, November 25, 2008, 1:45 PM
On Tue, Nov 25, 2008, oguz gurbulak wrote:
>
> 11
> check OAS ( I got some errors and warnings )
*What* errors and warnings?
> 12
> saveamberparams OAS h.prmtop h.inpcrd ( leap couldn't create input
> files )
Why not? What were the output messages?
Basically, all you have said is "leap didn't work..." without
giving any of
the error messages you received.
[A *very wild* guess: Be sure you have TER cards between each
separate molecule in the input pdb
file.]
...dac
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Received on Fri Dec 05 2008 - 18:27:21 PST
