Dear Dave,
Many thanks for the reply. I get the following errors while installing shifts:
$ make install
mkdir bin
cd src; make install
make[1]: Entering directory `/home/siavoush/programs/shifts-4.3/src'
nab -c shifts.nab
./nab2c: No such file or directory
nab2c failed!
make[1]: *** [shifts.o] Error 1
make[1]: Leaving directory `/home/siavoush/programs/shifts-4.3/src'
make: *** [install] Error 2
I have already set the $SHIFTSHOME environmental variable and also added the following lines to my .bashrc file:
export PATH=$PATH:/share/apps/amber11/AmberTools/src/nab
export PATH=$PATH:/share/apps/amber11/bin
Am I missing something?
Thanks in advance for your help.
Cheers, Siavoush
________________________________
From: case [mailto:case.biomaps.rutgers.edu]
Sent: Sat 2011/08/06 07:32 È.Ù
To: AMBER Mailing List
Subject: Re: [AMBER] Chemical shift restraints
On Sat, Aug 06, 2011, Siavoush Dastmalchi wrote:
>
> I am trying to do NMR refinement on the structure I have built by
> homology modeling. The NMR data are not complete and I don't have NOE
> data. What I was able to get out of NMR studies are some chemical shifts
> (1H, 13C, and 15N) and PHI and PSI angles predicted based on backbone
> chemical shifts using TALOS. I know that TALOS predicted angles are
> telling the same information embedded in chemical shifts, but was
> wondering how I can use makeSHF or fantasian (in fact the latter one is
> working on my system) to prepare Chemical shift restraints input file
> for the MD run.
Note that fantasian is designed for pseudocontact shifts in paramagnetic
molecules. Is this your situation?
The makeSHF program is very old, and is no longer distributed with Amber.
The "shifts" program (see
http://casegroup.rutgers.edu) can be used to
create input files, although it is admittedly more difficult than it
should be. There is an example in $AMBERHOME/test/rdc (look for the
Run.shifts command).
Note that this applies only to proton shifts; Amber has no facility to
directly incorporate carbon or nitrogen shifts in refinement. You might want
to look at xplor-nih, which does have such capability.
....dac
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Received on Sat Aug 06 2011 - 23:30:03 PDT
