Parse error in Autodock Vina
Hi,
The following error arises, when I use Vina. "ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive."
How to fix this error?
Thank you
autodock
docking
• 2,217 views
•
link
updated
by
Ram
•
written
by
bhavya2269 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Doubt on protein preparation before Vina
written by Ria •Im preparing protein using autodock for docking in vina. But during the step of repairing missing atom, some error came (a python shell) and that …
-
Problems in Molecular Docking in Autodock vina
written by Nibedita •How can I resolved this error in vina? Parse error on line 29 in file "ligand.pdbqt": ATOM syntax incorrect: "B" is not a valid AutoDock …
-
Autodock Vina not recognizing Chloride ion in ligand.pqbqt file
written by Sanjukta •Hi there, I am performing AutoDock Vina using command prompt, and running it for 10 ligands. My code is not able to run Ligands that …
-
How to dock compounds with Si to a protein using Autodock vina?
written by Akhilesh •I have been trying to dock compounds consisting silicon(Ex-Octaphenylsilsesquioxane) with a protein but Pyrx throws up an error saying "Si" is not a valid Autodock …
-
Stage 8 error on Desmond
written by bhavya2269 •Hi, The following error arises, when I use Desmond. `Stage 8 died due to backend error.` ``` Multisim summary (Thu Mar 9 10:07:24 2023): Stage …
-
biomaRt::getSequence - Invalid type argument
written by mbk0asisHi, all! I'm trying to download peptide sequence using `biomaRt::getSequence()` function. The code I used is like below, ```r seq = getSequence(id = c("ENSP00000367848"), type …
-
Problems with sdf to pdb file conversion
written by mlovelace713 •Hello, my name is Matthew Lovelace, I am a highschooler and for one of my classes I am working on a project that uses Autodock …
-
Visualising BedGraph files on UCSC [custom tracks]
written by anu014Hi all! How to add custom tracks to UCSC microbes, specifically for Mycobacterium Tuberculosis : http://microbes.ucsc.edu/cgi-bin/hgTracks?db=mycoTube_H37RV&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr%3A10001-35000&hgsid=2721963_tz9eJcUdmBnkbQWUpERSIVCYXdeZ Please note my file is BedGraph file which looks …
-
Load BED file on UCSC
written by maude •Hi everyone! I have a BED file that I'm trying to load on UCSC but I don't understand why it's not working. My BED file …
-
DISAPPEARANCE OF .PDBQT FILES
written by irfanpharmacist •Why .pdbqt files have disappeared from mgl tools folder 1.5.6 ? I am using autidock vina? after preparing .pdbqt files ,when i am going to …
google search: https://www.researchgate.net/post/How_to_add_atom_types_in_Autodock_Vina