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Hi, I was downloading namd2.exe and got this "Charm++ fatal error: FATAL ERROR: No simulation config file specified on command line."

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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😥

Too much noice kindly make all videos on namd and vmd in less noice environment

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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!

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Well done ....

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How many times it needs

Dr Sundas Iqbal has said very wonderful things,she is a very gentle and remarkable lady .She is very kind and good natured doctor.

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

Hello brother h r u . I need your help if you can share your I'd or Whatsapp contact I need your help indeed

Very very very nice 👌

Keep growing Sameen ❤️🎉

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 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

Respected Ma'am 💖

✋ Promo>SM.

Doctor sundas spoke very well,she is great human and great doctor

Thanks for sharing your views

Well said ,"corruption free Pakistan" should be the aim.