[AMBER] Analyzing the aMD results - Tutorial 22

From: carmine marco morgillo <FnTcy.hotmail.it>
Date: Sat, 19 Aug 2017 15:51:37 +0000

Dear Amber users,


I am trying to apply to my system the analysis scheme described in the tutorial 22 of the accelerated MD.

In particular I would like to compare the PC of the unbiased and accelerated MD on my system. I have run an unbiased trajectory of 1000 ns and two accelerated MD of 100 ns using different alphaP and alphaD values.
Following the tutorial I am stucked in the part of the generation and analysis of PCs. Using the suggested scripts (adapted to my system) I am encountering this error: No 'name <modes data set name>' argument given. Could not setup analysis [modes]

I am using ambertools 15. This is the log file produced by cpptraj:

Reading 'prmtop_now.prmtop' as Amber Topology
INPUT: Reading Input from STDIN
  [trajin amd_c100ns.binpos]
Reading 'amd_c100ns.binpos' as BINPOS
975 atoms, framesize=11704, filesize=11704000, #Frames=1000
Warning: Box information present in parm but not in trajectory.
Warning: DISABLING BOX in parm 'prmtop_now.prmtop'!
  [reference ../tent4now_eq.pdb ]
Reading '../tent4now_eq.pdb' as PDB
Warning: In PDB file tent4now_eq.pdb: 40 name mismatches with parm prmtop_now.prmtop.
  [rms reference mass :2-9,11-19,23-30&!.H= out rms_mass.agr]
Reference mask: [:2-9,11-19,23-30&!.H*](492)
    RMSD: (:2-9,11-19,23-30&!.H*), reference is "tent4now_eq.pdb" (:2-9,11-19,23-30&!.H*), with fitting, mass-weighted.
  [matrix covar name matrixdat .P,N4 out covmat-bb.dat]
    MATRIX: Calculating covariance matrix, output is by atom.
Printing to file covmat-bb.dat
Matrix data set is 'matrixdat'
Start: 1 Stop: Final frame
Mask1 is '.P,N4'
  [analyze matrix matrixdat out evecs-bb.dat vecs 50]
Changed DataFile 'evecs-bb.dat' type to Evecs file for set Modes_00003
    DIAGMATRIX: Diagonalizing matrix matrixdat and writing modes to evecs-bb.dat
Calculating 50 eigenvectors
  [analyze matrix matrixdat name evecs-bb vecs 50]
    DIAGMATRIX: Diagonalizing matrix matrixdat
Calculating 50 eigenvectors
Storing modes with name: evecs-bb
  [analyze modes fluct out analyzemodesflu.dat modes evecs-bb beg 1 end 50]
Error: No 'name <modes data set name>' argument given.
Error: Could not setup analysis [modes]
1 errors encountered reading input.

Any help is appreciated.


Carmine


******************************
Carmine Marco Morgillo, PhD
Dipartimento di Farmacia
FacoltÓ di Farmacia
UniversitÓ di Napoli "Federico II"
Via D. Montesano, 49
80131 Napoli
fntcy.hotmail.it<mailto:fntcy.hotmail.it>
carminemarco.morgillo.unina.it
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Received on Sat Aug 19 2017 - 09:00:03 PDT
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