AMBER Archive (2009)

Subject: Re: [AMBER] Problem with Nmode

From: Kshatresh Dutta Dubey (kshatresh_at_gmail.com)
Date: Thu May 21 2009 - 00:14:50 CDT

Dear David Sir,
When I modified ntx=0 to 1 and ntxo=0 to 1 in mm_pbsa_createinput.pm my
problem got solved, i.e. nmode is running properly. But i am not sure that
it is a correct method or not.
Kindelly make sure me that it is a right or wrong.
Regards
Kshatresh

On Wed, May 20, 2009 at 11:32 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Tue, May 19, 2009, Kshatresh Dutta Dubey wrote:
> >
> > At line 34 of file _getcor.f
> > Fortran runtime error: End of file
> > /usr/local/amber10/exe/nmode -O -i nmode_lig.in -o nmode_lig.1.out -c
> > sanmin_lig.1.restrt -p ../STI.top not running properly
>
> A guess: you have told nmode that a binary form of coordinates is being
> used,
> but the sanmin_lig.1.restrt file may be formatted.
>
> General advice: Be sure you have installed bugfix.17, make sure the test
> cases work, and compare your inputs to those in the test cases.
>
> [If there is anyone on the list willing to really check out what the
> mm_pbsa
> scripts are doing, and to improve them, that would be welcome. We've been
> getting lots of user complaints.]
>
> ...dac
>
>
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