Dear Experts,
I want to create an rst7 file for restarting a simulation from between my
trajectory.
My initial systems have been generated with CHARMM-GUI, with Charmm36 force
field.
I have followed the following guidance (
http://archive.ambermd.org/201506/0097.html), however, I am getting the
following error:
===============
(base) [Prathit.master]~/APP/OnlyAPP/AlphaFold2/770_res/Charmm-Gui_Dimer-units/E1-E2_75Aenm/charmm-gui-3765059778/amber>cpptraj
-p step3_input.parm7 -y step5_prot.4_frame2.pdb -x step5_prot.4_frame2.rst7
CPPTRAJ: Trajectory Analysis. V4.25.6
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 07/26/22 19:58:00
| Available memory: 12.294 GB
Reading 'step3_input.parm7' as Amber Topology
CHAMBER topology:
CHARMM36 All-atom Force Field
Warning: Amber topology flag 'CMAP_COUNT' is unrecognized and will be
skipped.
Warning: Amber topology flag 'CMAP_RESOLUTION' is unrecognized and will be
skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_01' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_02' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_03' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_04' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_05' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_INDEX' is unrecognized and will be
skipped.
Reading 'step5_prot.4_frame2.pdb' as PDB
Read CRYST1 info from PDB: a=240.854 b=240.854 c=240.854 alpha=90
beta=90 gamma=90
Error: PDB step5_prot.4_frame2.pdb: No frames read. atom=8418 expected
1394424.
Error: Could not set up 'step5_prot.4_frame2.pdb' for reading.
Error: Could not set up input trajectory 'step5_prot.4_frame2.pdb'.
TIME: Total execution time: 2.6554 seconds.
Error: Error(s) occurred during execution.
===============
If you have any suggestions/flow-lines, please let me know kindly.
Any help will be deeply appreciated.
Thank you,
Sincerely,
Prathit
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Received on Thu Aug 04 2022 - 13:37:28 PDT
