Thanks David for your reply,
but it already stands LISTIN= POUT in sander run.
My output file doesn't correspond to RST file. So My guess something happends during minimization. Can you please take a look?
I attached both.
Thank you,
Olena
________________________________________
From: David A. Case [case.biomaps.rutgers.edu]
Sent: 08 February 2012 01:56
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER minimization
On Tue, Feb 07, 2012, Olena Dobrovolska wrote:
>
> I have performed a minimization of my protein based on NMR
> restraints. But final output file has lines like this:
>
>
> O ILE 16 -- O HID 17: 4.338 4.110 0.228 1.041 d 135: 0
> Does anybody have a suggesstion where the oxygen atoms come from (I
> expect there protons instead)? I guess this contributes to the energy
> value and distance penalties (which are quite high).
They must be coming from your input NMR restraints in some fashion. If you
add LISTIN=POUT to your run, you will get lots of debugging information about
each restraint. That should help you find out what is happening.
Or, find the atom numbers for O in residues and 17, and look in your restraint
files for those atom numbers. A lot depends on how you creating the DISANG
file in the first place.
....dac
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- application/octet-stream attachment: RST.dist
Received on Wed Feb 08 2012 - 04:30:04 PST
