On Mon, Aug 15, 2005, sebnem wrote:
> I need to carry a molecule from nmode (amber 7), where i carried out NMA
> analysis, to sander(amber 7). However when I take the minimized structure
> from nmode, i am getting a different non-bonded energy term in sander.
>
> Here is the input of nmode:
> minimization,
> &data
> ntrun=4,
> cut=9999.0
> nprint=100,
> drms=0.00000001,
> maxcyc=2,
> scnb=2.0,
> scee=1.2,
> ibelly=1,
> idiel=1,
> &end
> group info
> RES 1 34
> END
> END
I think the belly option is implemented differently in nmode and in current
versions of sander. This means that some terms that would be fixed are
eliminated from nmode but not from sander.
Try to run without the belly option to see if this helps clear things up.
....good luck...dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Aug 17 2005 - 17:53:01 PDT
