@@trendsinwomen Unfortunately I tried restart my run like what you did in 19:50. I received "Fatal error: Error reading extended system file". How should I proceed?
The content of the step5_production.restart file looked weird: # NAMD extended system configuration restart file #$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w 2150000 nan nan nan nan nan nan nan nan nan 0.185578688979 0.0552813336253 0.0134596358985 nan nan nan nan nan nan
Thanks a lot for the video. Your installation is in windows but in real life, using Linux and a GPU computer only give us reach biologically relevant timescales. Most of the MD community uses Linux. It will be actually useful if you can make a tutorial video on namd installation on GPU ubuntu
Thank you so much for the comments. As per my expertise I prepared tutorial for windows setup installation to perform MD simulations. May be in future I would like to make it for ubuntu using GROMACS.
Nicely explained! I had a query regarding the input files, can we not use only the final coordinate or velocity files for example .coor instead of restart.coor files
thanks for the tutorial, i am trying to generate gromacs input files for my docked system, but the error comes Output Excerpt from step1_pdbreader.out: CHARMM> patch GLUP PROB 128 setup warn ATOM PROB GLU 128 HE2 ADDED. Message from MAPIC: Atom numbers are changed. AUTGEN: Autogenerating specified angles and dihedrals. AUTOGEN: 20 angles are removed before regeneration for selected atoms. AUTOGEN: 16 dihedrals are removed before regeneration for selected atoms. PATCH: Check angles and dihedrals autogenerated. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 2 Number of residues = 688 Number of atoms = 10823 Number of groups = 3326 Number of bonds = 10929 Number of angles = 19739 Number of dihedrals = 28910 Number of impropers = 1792 Number of cross-terms = 684 Number of autogens = 0 Number of HB acceptors = 986 Number of HB donors = 1205 Number of NB exclusions = 0 Total charge = 19.00000 CHARMM> CHARMM> autogenerate on AUTOGEN: turned on for selected atoms. CHARMM> autogenerate angles dihedrals AUTGEN: Autogenerating specified angles and dihedrals. AUTOGEN: 19739 angles are removed before regeneration for selected atoms. AUTOGEN: 28910 dihedrals are removed before regeneration for selected atoms. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 2 Number of residues = 688 Number of atoms = 10823 Number of groups = 3326 Number of bonds = 10929 Number of angles = 19739 Number of dihedrals = 28910 Number of impropers = 1792 Number of cross-terms = 684 Number autogens = 0 Number of HB acceptors = 986 Number of HB donors = 1205 Number of NB exclusions = 0 Total charge = 19.00000 CHARMM> CHARMM> open read card unit 10 name dimerdock2_heta.crd OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 10 with status "KEEP" VOPEN> Attempting to open::dimerdock2_heta.crd:: OPNLGU> Unit 10 opened for READONLY access to dimerdock2_heta.crd Conversation with Gemini profile picture Imagine three different experts are answering this question. All experts will write down 1 step of their thinking, then share it with the group. Then all experts will go on to the next step, etc. If any expert realises they're wrong at any point then they leave. The question is... Simulate three brilliant, logical experts collaboratively answering a question. Each one verbosely explains their thought process in real-time, considering the prior explanations of others and openly acknowledging mistakes. At each step, whenever possible, each expert refines and builds upon the thoughts of others, acknowledging their contributions. They continue until there is a definitive answer to the question. For clarity, your entire response should be in a markdown table. The question is... Identify and behave as three different experts that are appropriate to answering this question. All experts will write down the step and their thinking about the step, then share it with the group. Then, all experts will go on to the next step, etc. At each step all experts will score their peers response between 1 and 5, 1 meaning it is highly unlikely, and 5 meaning it is highly likely. If any expert is judged to be wrong at any point then they leave. After all experts have provided their analysis, you then analyze all 3 analyses and provide either the consensus solution or your best guess solution. The question is [ Suspected reasons for this error: { Output Excerpt from step1_pdbreader.out: CHARMM> patch GLUP PROB 128 setup warn ATOM PROB GLU 128 HE2 ADDED. Message from MAPIC: Atom numbers are changed. AUTGEN: Autogenerating specified angles and dihedrals. AUTOGEN: 20 angles are removed before regeneration for selected atoms. AUTOGEN: 16 dihedrals are removed before regeneration for selected atoms. PATCH: Check angles and dihedrals autogenerated. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 2 Number of residues = 688 Number of atoms = 10823 Number of groups = 3326 Number of bonds = 10929 Number of angles = 19739 Number of dihedrals = 28910 Number of impropers = 1792 Number of cross-terms = 684 Number of autogens = 0 Number of HB acceptors = 986 Number of HB donors = 1205 Number of NB exclusions = 0 Total charge = 19.00000 CHARMM> CHARMM> autogenerate on AUTOGEN: turned on for selected atoms. CHARMM> autogenerate angles dihedrals AUTGEN: Autogenerating specified angles and dihedrals. AUTOGEN: 19739 angles are removed before regeneration for selected atoms. AUTOGEN: 28910 dihedrals are removed before regeneration for selected atoms. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 2 Number of residues = 688 Number of atoms = 10823 Number of groups = 3326 Number of bonds = 10929 Number of angles = 19739 Number of dihedrals = 28910 Number of impropers = 1792 Number of cross-terms = 684 Number of autogens = 0 Number of HB acceptors = 986 Number of HB donors = 1205 Number of NB exclusions = 0 Total charge = 19.00000 CHARMM> CHARMM> open read card unit 10 name dimerdock2_heta.crd OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 10 with status "KEEP" VOPEN> Attempting to open::dimerdock2_heta.crd:: OPNLGU> Unit 10 opened for READONLY access to dimerdock2_heta.crd CHARMM> read sequence coor card unit 10 resid **** Warning **** The following extraneous characters were found while command processing in CHARMM CARD MAINIO> Sequence information being read from unit 10. TITLE> 23 EXT RDTITL> No title read. RESIDUE SEQUENCE -- 1 RESIDUES LIG CHARMM> generate HETA setup warn first none last none ***** ERROR in GENIC ***** Residue 'LIG ' was not found. Can you please troubleshoot it for me😥
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Thanks so much! Your tutorial is the only one that showed how to RESTART a aborted run! You're a lifesaver!
You are welcome!
@@trendsinwomen Unfortunately I tried restart my run like what you did in 19:50. I received "Fatal error: Error reading extended system file". How should I proceed?
The content of the step5_production.restart file looked weird:
# NAMD extended system configuration restart file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w
2150000 nan nan nan nan nan nan nan nan nan 0.185578688979 0.0552813336253 0.0134596358985 nan nan nan nan nan nan
@@Drpokok90 what is your OS? Windows 10?
@@trendsinwomen yes. Windows 10
Thanks a lot for the video. Your installation is in windows but in real life, using Linux and a GPU computer only give us reach biologically relevant timescales. Most of the MD community uses Linux. It will be actually useful if you can make a tutorial video on namd installation on GPU ubuntu
Thank you so much for the comments. As per my expertise I prepared tutorial for windows setup installation to perform MD simulations. May be in future I would like to make it for ubuntu using GROMACS.
Nicely explained! I had a query regarding the input files, can we not use only the final coordinate or velocity files for example .coor instead of restart.coor files
For restart .coor files only
thanks for the tutorial, i am trying to generate gromacs input files for my docked system, but the error comes
Output Excerpt from step1_pdbreader.out:
CHARMM> patch GLUP PROB 128 setup warn
ATOM PROB GLU 128 HE2 ADDED.
Message from MAPIC: Atom numbers are changed.
AUTGEN: Autogenerating specified angles and dihedrals.
AUTOGEN: 20 angles are removed before regeneration for selected atoms.
AUTOGEN: 16 dihedrals are removed before regeneration for selected atoms.
PATCH: Check angles and dihedrals autogenerated.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 2 Number of residues = 688
Number of atoms = 10823 Number of groups = 3326
Number of bonds = 10929 Number of angles = 19739
Number of dihedrals = 28910 Number of impropers = 1792
Number of cross-terms = 684 Number of autogens = 0
Number of HB acceptors = 986 Number of HB donors = 1205
Number of NB exclusions = 0 Total charge = 19.00000
CHARMM>
CHARMM> autogenerate on
AUTOGEN: turned on for selected atoms.
CHARMM> autogenerate angles dihedrals
AUTGEN: Autogenerating specified angles and dihedrals.
AUTOGEN: 19739 angles are removed before regeneration for selected atoms.
AUTOGEN: 28910 dihedrals are removed before regeneration for selected atoms.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 2 Number of residues = 688
Number of atoms = 10823 Number of groups = 3326
Number of bonds = 10929 Number of angles = 19739
Number of dihedrals = 28910 Number of impropers = 1792
Number of cross-terms = 684 Number
autogens = 0
Number of HB acceptors = 986 Number of HB donors = 1205
Number of NB exclusions = 0 Total charge = 19.00000
CHARMM>
CHARMM> open read card unit 10 name dimerdock2_heta.crd
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 10 with status "KEEP"
VOPEN> Attempting to open::dimerdock2_heta.crd::
OPNLGU> Unit 10 opened for READONLY access to dimerdock2_heta.crd
Conversation with Gemini
profile picture
Imagine three different experts are answering this question. All experts will write down 1 step of their thinking, then share it with the group. Then all experts will go on to the next step, etc. If any expert realises they're wrong at any point then they leave. The question is...
Simulate three brilliant, logical experts collaboratively answering a question. Each one verbosely explains their thought process in real-time, considering the prior explanations of others and openly acknowledging mistakes. At each step, whenever possible, each expert refines and builds upon the thoughts of others, acknowledging their contributions. They continue until there is a definitive answer to the question. For clarity, your entire response should be in a markdown table. The question is...
Identify and behave as three different experts that are appropriate to answering this question.
All experts will write down the step and their thinking about the step, then share it with the group.
Then, all experts will go on to the next step, etc.
At each step all experts will score their peers response between 1 and 5, 1 meaning it is highly unlikely, and 5 meaning it is highly likely.
If any expert is judged to be wrong at any point then they leave.
After all experts have provided their analysis, you then analyze all 3 analyses and provide either the consensus solution or your best guess solution.
The question is [ Suspected reasons for this error: { Output Excerpt from step1_pdbreader.out:
CHARMM> patch GLUP PROB 128 setup warn
ATOM PROB GLU 128 HE2 ADDED.
Message from MAPIC: Atom numbers are changed.
AUTGEN: Autogenerating specified angles and dihedrals.
AUTOGEN: 20 angles are removed before regeneration for selected atoms.
AUTOGEN: 16 dihedrals are removed before regeneration for selected atoms.
PATCH: Check angles and dihedrals autogenerated.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 2 Number of residues = 688
Number of atoms = 10823 Number of groups = 3326
Number of bonds = 10929 Number of angles = 19739
Number of dihedrals = 28910 Number of impropers = 1792
Number of cross-terms = 684 Number of autogens = 0
Number of HB acceptors = 986 Number of HB donors = 1205
Number of NB exclusions = 0 Total charge = 19.00000
CHARMM>
CHARMM> autogenerate on
AUTOGEN: turned on for selected atoms.
CHARMM> autogenerate angles dihedrals
AUTGEN: Autogenerating specified angles and dihedrals.
AUTOGEN: 19739 angles are removed before regeneration for selected atoms.
AUTOGEN: 28910 dihedrals are removed before regeneration for selected atoms.
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 2 Number of residues = 688
Number of atoms = 10823 Number of groups = 3326
Number of bonds = 10929 Number of angles = 19739
Number of dihedrals = 28910 Number of impropers = 1792
Number of cross-terms = 684 Number of autogens = 0
Number of HB acceptors = 986 Number of HB donors = 1205
Number of NB exclusions = 0 Total charge = 19.00000
CHARMM>
CHARMM> open read card unit 10 name dimerdock2_heta.crd
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 10 with status "KEEP"
VOPEN> Attempting to open::dimerdock2_heta.crd::
OPNLGU> Unit 10 opened for READONLY access to dimerdock2_heta.crd
CHARMM> read sequence coor card unit 10 resid
**** Warning **** The following extraneous characters
were found while command processing in CHARMM
CARD
MAINIO> Sequence information being read from unit 10.
TITLE> 23 EXT
RDTITL> No title read.
RESIDUE SEQUENCE -- 1 RESIDUES
LIG
CHARMM> generate HETA setup warn first none last none
***** ERROR in GENIC ***** Residue 'LIG ' was not found.
Can you please troubleshoot it for me😥
my command prompt wont recognise the namd code even though i downloaded like in the video, please could you help? thankyou, its for my dissertation
Contact me at email jcsccfana@yahoo.com send me screenshot
Too much noice kindly make all videos on namd and vmd in less noice environment
Ok. Noted
Hi, I was downloading namd2.exe and got this "Charm++ fatal error:
FATAL ERROR: No simulation config file specified on command line."
Edit environment variable add path of NAMD there
How many times it needs
What times? Please explain