I have problem in running NAMD, it usually display fatal error message " No simulation config file specified on command line" despite the fact that I have installed the mpi_x64.msi.
I want to perform MD simulation of protein-ligand complex using VMD-NAMD. When I want to create protein structure file (PSF), there is dialogue box asking me to parameterize my ligand.
08 September 2016 4,988 5 View
I want to perform simulation and when I run the command prompt window with the following syntax " namd2 ubq_ws_eq.conf > ubq_ws_eq.log &" below error will appear" Charm++ fatal error:FATAL...
06 July 2016 1,238 19 View
I have tried several times to access this server (http://www.ddg-pharmfac.net/vaxijen/), but I could not. Can anyone help me with appropriate link to this server
06 July 2016 8,765 2 View
I want to build a model of query sequence (qseq) based on the alignment against the multiple templates using the `model_mult.py'. from modeller import *from modeller.automodel import * env =...
05 June 2016 5,309 4 View
I have a protein sequence but I checked PDB for the purpose comparative modeling, but I couldn't find any similar protein with known 3D structure, yet I want model my protein. Beside ITASSER which...
04 May 2016 7,622 4 View
Why do we need molecular dynamic simulation of protein-ligand complex? what is the important
04 May 2016 3,662 0 View
BIOINFORMATICS
04 May 2016 614 4 View
Hi, I have a question about normalizing the MTT OD values for doing the statistical analysis. So, if we have 3 different plates and we call them 3 different replicates, so, first we would...
07 August 2024 8,106 4 View
Dear QE-users, In the method where full MS positive mode and PRM mode are used, we always get an incorrect auxiliary gas reading (41 instead of 25). This only happens in this method; other...
06 August 2024 4,953 0 View
I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...
04 August 2024 1,200 2 View
Hello guys! Do you have experience running a Oaxaca-Blinder decomposition on R applying person weights. How do you suggest doing it? I have a variable PERWT which gives more information on how...
04 August 2024 6,033 0 View
I would like to perform transfection with the reagent DharmaFECT Duo (Horizon) on the AGS cell line. Could you please inform me of the optimal concentration to use without causing cytotoxicity in...
03 August 2024 3,851 1 View
Hi there! I recently started working on Lx-2 cells. When I thaw the cells, they start attaching within few hours but later in about 2 days they started rounding and dying. I used DMEM+2% FBS...
31 July 2024 3,893 0 View
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31 July 2024 1,671 3 View
Hi all, may I ask you for advice about treating monolayer culture cell line with essential oil. Due to the hydrophobic character of the oil, I am concerning how can it equally affect to all the...
31 July 2024 5,301 2 View
Hello Everyone I have a question about structure for connectivity analysis on sources. My goal: preprocess and cut data into trials create headmodels, using template MRI file perform source...
30 July 2024 2,744 1 View
When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!
29 July 2024 488 0 View