Dear List,
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. I searched the archive to get some practical instruction on how to generate chemical shift restraints, but couldn't find one. The tutorial on "Refinement of a DNA Duplex" was useful and I used it to prepare torsion angle restraints input file.
When I use "fantasian" it asks me several questions and I provide the answer but not sure if I am doing it right. Here are the inputs:
Amber11 Module: fantasian
This is Fantasian VERSION 2.0 - Nov 1999
Name of observed shifts input file:
chemshift.cs => this is a 5 column file each line is like this: 3 174.820 0.031 CO 3
chemshift.cs
Name of Amber pdb input file: => this is a pdb file generated by Amber
cehlim_amber.pdb
cehlim_amber.pdb
Name for observed out file: => Not sure, assuming Fantasian will generate this
obs.out
obs.out
Name for output file: => Not sure, assuming Fantasian will generate this
out.out
out.out
Number of atoms in each structure (not more than 4000 ):
2569
2569
Number of structures (not more than 40 ):
10
10
Number of paramagnetic ions (not more than 5 ): I have 4 Zn ions and was assuming I should give this a zero, but it doesn't accept it
4
4
Insert atom number corresponding to paramagnetic ion # 1
2566
2566
Insert atom number corresponding to paramagnetic ion # 2
2567
2567
Insert atom number corresponding to paramagnetic ion # 3
2568
2568
Insert atom number corresponding to paramagnetic ion # 4
2569
2569
Value of tolerance (0-1): => not sure about this
0.5
0.500
Would you define reference system(s)? (y/n) => not sure about this
n
n
Number of computed solutions:
10
10
------------ S T A R T -------------
***** READING OBSERVED SHIFT:
forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
Image PC Routine Line Source
libintlc.so.5 00002AB9CE3B5AB1 Unknown Unknown Unknown
libintlc.so.5 00002AB9CE3B4A85 Unknown Unknown Unknown
libifcore.so.5 00002AB9CDCF4B43 Unknown Unknown Unknown
I will appreciate it if I get some help on this.
Cheers, Siavoush
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Received on Sat Aug 06 2011 - 04:00:02 PDT
