I've received an error in NMA-DIMB method , could you suggest me how to solve this issue?. Detailed output is attached in a file "a.txt". A brief look at the output file has the following error,
NMDIMB: Iteration number = 0 NMDIMB: Dimension of the reduced basis set = 54 NMDIMB: 54 modes are saved in unit 20
***** LEVEL -3 WARNING FROM ***** ***** There are less than six Trans-Rot vectors ****************************************** BOMLEV ( -2) IS REACHED - TERMINATING. WRNLEV IS 5
Here is the input informations:
I have a protein of 23970 atoms and 1480 residues. The system has following details, Number of segments = 1 Number of residues = 1480 Number of atoms = 23970 Number of groups = 7331 Number of bonds = 24210 Number of angles = 43853 Number of dihedrals = 64185 Number of impropers = 3822 Number of cross-terms = 0 Number of HB acceptors = 2175 Number of HB donors = 2657 Number of NB exclusions = 0 Total charge = 19.00000.
I have the charmm executable with following stack/heap size ,
1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 35b1 August 15, 2008 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.6.32-279.2.1.el6.x86_64(x86_64)@loca Created on 7/15/13 at 11:49:52 by user: saravana
Maximum number of ATOMS: 200000, and RESidues: 80000 Current HEAP size: 81520000, and STACK size: 80000000
The commnd that I used for DIMB-nma analysis is ,
OPEN WRITe FILE UNIT 20 NAME initial1cp.bas VIBRan NMODes 100 DIMB ITERations 0 PARDim 50 IUNMode 20 BIG END
!Do the iterative diagonalization, using the precalculated initial !basis of 53 vectors. 53 converged modes will be written to unit 10:
OPEN READ FILE UNIT 20 NAME initial1cp.bas OPEN WRITe FILE UNIT 10 NAME modes1cp.mod VIBRan NMODes 53 DIMB ITERations 100 TOLErance 0.05 PARDim 30 - IUNMode 10 IUNRead 20 DWIN END
FLUCT ATOM MODE 1 THRU 13 TEMP 300 SELE ALL END FLUCT ATOM MODE 1 THRU 13 RMS SELE ALL END PRINt NORM VECTOR DIPOLE FLUCtuations RMS FLUCT ATOM MODE 1 THRU 13 RMS 0.2 SELE ALL END FLUCT ATOM MODE 1 THRU 13 TEMP 300.0 SELE ALL END PRINt NORM VECTOR DIPOLE FLUCtuations TEMP 300 RMS PRINt NORM VECTOR DIPOLE FLUCtuations TEMP 300
Don't run with bomlev -2 ... it is unnecessary and may mask errors that are pertinent to your problem. In general, it is best practice to run with bomlev 0 with few exceptions.
Is your structure well minimized? If not, the translational and rotational motions will be spread out among multiple modes. I am not too familiar with how DIMB works, but it seems like this might be your problem. Given that you are seeing negative frequencies in your output file (as far as I can tell), this seems like the first thing to try.