This collective variable calculates a scoring function based on the comparison of backcalculated and experimental backbone chemical shifts for a protein (CA, CB, C', H, HA, N).

CamShift [8] is employed to back calculate the chemical shifts that are then compared with a set of experimental values to generate a score [13] [Granata:2013dk.]

It is also possible to backcalculate the chemical shifts from multiple replicas and then average them to perform Replica-Averaged Restrained MD simulations [5] [Camilloni:2013hs.]

HOW TO COMPILE IT

In general the system for which chemical shifts are to be calculated must be completly included in ATOMS. It should also be made WHOLE before the the backcalculation. CamShift is included in the free package ALMOST v.2.1 that can be dowload via SVN (svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code). ALMOST 2.1 can be found in branches/almost-2.1/ and it can be compiled:

./configure
make

Once the code is compiled you should see the ALMOST library libAlm.a in src/lib/

PLUMED 2 must then be compiled by linking ALMOST:

in DYNAMIC_LIBS the following paths should be added:

-L/ALMOST_BASE_PATH/branches/almost-2.1/src/lib -lAlm \
-L/ALMOST_BASE_PATH/branches/almost-2.1/lib/sqlite-3.6.23.1 -lsqlite3 -lz -lbz2 \
-L/ALMOST_BASE_PATH/branches/almost-2.1/src/forcefield -lnbimpl \
-L/ALMOST_BASE_PATH/branches/almost-2.1/src/lib/modules -lshx

and in CPPFLAGS

-I/ALMOST_BASE_PATH/almost/branches/almost-2.1/include \
-I/ALMOST_BASE_PATH/almost/branches/almost-2.1/include/almost \
-I/ALMOST_BASE_PATH/almost/branches/almost-2.1/lib/sqlite-3.6.23.1 -D__PLUMED_HAS_ALMOST

with ALMOST_BASE_PATH the full path to the ALMOST folder

HOW TO USE IT

To use CamShift as a restraint or as collective variable or as a replica-averaged restraint first of all the experimental data are needed. CamShift uses backbone and Cb chemical shifts that must be provided as text files:

CAshifts.dat:
CBshifts.dat:
Cshifts.dat:
Hshifts.dat:
HAshifts.dat:
Nshifts.dat:
#1 0.0
2 55.5
3 58.4
.
.
#last 0.0
#last+1 (first) of second chain
.
#last of second chain

All of them must always be there. If a chemical shift for an atom of a residue is not available 0.0 must be used. So if for example all the Cb are not available all the chemical shifts for all the residues should be set as 0.0.

A template.pdb file is needed to the generate a topology of the protein within ALMOST. For histidines in protonation states different from D the HIE/HIP name should be used in the template.pdb. GLH and ASH can be used for the alternative protonation of GLU and ASP. Non-standard amino acids and other molecules are not yet supported! If multiple chains are present the chain identifier must be in the standard PDB format, together with the TER keyword at the end of each chain. Residues numbering should always go from 1 to N in both the chemical shifts files as well as in the template.pdb file. Two more keywords can be used to setup the topology: CYS-DISU to tell ALMOST to look for disulphide bridges and TERMINI to define the protonation state of the the chain's termini (currently only DEFAULT (NH3+, CO2-) and NONE (NH, CO)).

Two more standard files are also needed: an ALMOST force-field file, corresponding to the force-field family used in the MD code, (a03_cs2_gromacs.mdb for the amber family or all22_gromacs.mdb for the charmm family) and camshift.db, both these files can be copied from almost/branches/almost-2.1/toppar.

All the above files must be in a single folder that must be specified with the keyword DATA.

Examples

case 1:

WHOLEMOLECULES ENTITY0=1-174
cs: CS2BACKBONE ATOMS=1-174 DATA=data/ FF=a03_gromacs.mdb FLAT=0.0 NRES=13 ENSEMBLE
cse: RESTRAINT ARG=cs SLOPE=24 KAPPA=0 AT=0.
PRINT ARG=cs,cse.bias

case 2:

WHOLEMOLECULES ENTITY0=1-174
cs: CS2BACKBONE ATOMS=1-174 DATA=data/ FF=a03_gromacs.mdb FLAT=1.0 NRES=13 TERMINI=DEFAULT,NONE CYS-DISU WRITE_CS=1000
PRINT ARG=cs

(See also WHOLEMOLECULES, RESTRAINT and PRINT)