Dear Amber developers,
I am creating metal parameters for Mn using bonded model strictly
following tutorial
(
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm).
Everything has gone pretty fine, up until the very end, when an error
occurred when I tried to load my topology and coordinates into
cpptraj. The error is the same as it was specified in tutorial:
Error: Atom 7908 was assigned a lower molecule # than previous atom.
Error: This can happen if bond information is incorrect or missing, or if the
Error: atom numbering in molecules is not sequential. Try one of the
Error: following:
Error: - If this is a PDB file, try using the 'noconect' keyword.
Error: - If this topology did not have bond info, try increasing the bond
Error: search cutoff above 0.2 Ang. ('bondsearch <cutoff>').
Error: - Use the 'fixatomorder' command to reorder the topology and any
Error: associated coordinates.
Error: - Use the 'setMolecules' command in parmed to reorder only the
Error: topology.
Error: Could not determine molecule information for metal_solv.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for metal_solv.prmtop.
I followed the advices about fixing atom order given in tutorial and
http://archive.ambermd.org/201507/0402.html. This is my script for
fixing atom order:
fixatomorder outprefix fixed
trajin metal_solv.inpcrd
trajout fixed.metal_solv.inpcrd
run
quit
I run this script using command:
cpptraj -p metal_solv.prmtop -i fixatord.in > fixatord.out
The output file is as follows:
Reading 'metal_solv.prmtop' as Amber Topology
INPUT: Reading input from 'fixatord.in'
[fixatomorder outprefix fixed]
Warning: Action specified before trajin/ensemble. Assuming trajin.
FIXATOMORDER: Will attempt to fix atom ordering when atom numbering
in molecules is non-sequential.
Re-ordered topology will be output with prefix fixed
[trajin metal_solv.inpcrd]
Reading 'metal_solv.inpcrd' as Amber Restart
[trajout fixed.metal_solv.inpcrd]
Warning: Format not specified and extension '.inpcrd' not recognized.
Defaulting to Amber Trajectory.
Writing 'fixed.metal_solv.inpcrd' as Amber Trajectory
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: metal_solv.prmtop, 64277 atoms, 19310 res, box: Orthogonal, 0 mol
INPUT TRAJECTORIES (1 total):
0: 'metal_solv.inpcrd' is an AMBER restart file, no velocities, Parm
metal_solv.prmtop (Orthogonal box) (reading 1 of 1)
Coordinate processing will occur on 1 frames.
OUTPUT TRAJECTORIES (1 total):
'fixed.metal_solv.inpcrd' (1 frames) is an AMBER trajectory
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'metal_solv.prmtop' (1 actions):
0: [fixatomorder outprefix fixed]
Detected 18799 molecules.
Re-ordered parm: 64277 atoms, 19310 res, box: Orthogonal,
18799 mol, 18783 solvent
Writing topology 0 (metal_solv.prmtop) to
'fixed.metal_solv.prmtop' with format Amber Topology
----- metal_solv.inpcrd (1-1, 1) -----
100% Complete.
Read 1 frames and processed 1 frames.
TIME: Avg. throughput= 2.6128 frames / second.
ACTION OUTPUT:
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 0.3827 s ( 97.59%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0094 s ( 0.02%)
TIME: Run Total 0.3922 s
---------- RUN END ---------------------------------------------------
The problem is, however, when I want to start running simulations,
beginning from minimization job, in the output following error is to
be found:
| ERROR: Could not read second line of fixed.metal_solv.inpcrd
| Bad inpcrd file!
First three lines of my fixed.metal_solv.inpcrd:
Cpptraj Generated trajectory
73.599 53.001 21.001 74.334 53.652 21.189 73.931 52.285 20.388 72.828
53.476 20.578 73.156 52.387 22.271 73.925 52.466 22.923 71.935 53.136
It seems to me as if Amber treats my fixed.metal_solv.inpcrd file as
it was trajectory instead of rst file, as it was also stated in
cpptraj output. Do you have any idea how can I prepare coordinate file
properly so there are no issues with numbering and the file could be a
starting point for following simulations?
Kind regards,
Szymon Zaczek
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Received on Mon Jul 17 2017 - 12:00:03 PDT
