CH3SHIFTS

This is part of the colvar module

This collective variable calculates a scoring function based on the comparison of calculated and experimental methyl chemical shifts.

CH3Shift [35] is employed to back calculate the chemical shifts of methyl groups (ALA:HB; ILE:HD,HG2; LEU:HD1,HD2; THR:HG2; VAL:HG1,HG2) that are then compared with a set of experimental values to generate a score [34] [21].

It is also possible to backcalculate the chemical shifts from multiple replicas and then average them to perform Replica-Averaged Restrained MD simulations [14] [16].

In general the system for which chemical shifts are to be calculated must be completly included in ATOMS. It should also be made whole WHOLEMOLECULES before the the back-calculation.

HOW TO COMPILE IT

Installing PLUMED with ALMOST on how to compile PLUMED with ALMOST.

HOW TO USE IT

CH3Shift reads from a text file the experimental chemical shifts:

CH3shifts.dat:
1.596 28
0.956 46
0.576 3 HG2
0.536 3 HD1
0.836 13 HG2
0.666 13 HD1
0.716 23 HG2
0.506 23 HD1

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)).

One more standard file is also needed, that is 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).

All the above files must be in a single folder that must be specified with the keyword DATA (multiple definition of the CV can point to different folders).

Examples

case 1:

WHOLEMOLECULES ENTITY0=1-174
cs: CH3SHIFTS 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: CH3SHIFTS 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)