vas penu

IndexError: index 188 is out of bounds for axis 0 with size 184

3

HI , I am getting following error, while doing msm analysis, Could you please suggest me how to fix this error ? Regards Vas --------------------------------------------------------------------------- IndexError Traceback (most recent call...

Error : model.viewStates(nucleic=True), not recognize the 'nucleic' parameter

4

I am currently engaged in conformational analysis for RNA using adaptive simulations. I've encountered an issue where the code does not recognize the 'nucleic' parameter in the snippet provided below....

3D FES profile

1

I am currently employing the following script to generate a Free Energy Surface (FES) profile, utilizing TICA-1 and TICA-2 as dimensions. Could I potentially integrate a third dimension into this...

Issues with equilibration phase (Protein-RNA-complex)

11

Hello, I am running MD simulation on Protein-DNA-RNA complex. However, The DNA and RNA are dissociated in first step of the Equilibration phase. Could you please advise on this matter...

RuntimeError (adaptive MD for RNA): when using a dihedral with an atom name containing a single quote

13

I encountered a RuntimeError when running the ad.run() function using a dihedral with an atom name containing a single quote (e.g., "O3'"). Here's the code I used: ```py atom1_alpha_Dihang_residue_6 =...

Subject: No Improvement in Validation Accuracy

1

Hi I'm reaching out to request your help to resolve with an issue we're encountering in the current project, specifically regarding the validation accuracy (acc_val) in our model's performance, which...

Reg : Amber / Charmm Force field parameters for ARG (mono-methyl, dimethyl (asym, sym)

2

Hi, I'm in search of force-field parameters for methyl modification of ARG (attached screenshot for your reference). Screenshot : (https://github.com/Acellera/htmd/assets/29959559/9edca9ad-6a46-4b1c-bd1c-3cf4f96846be) Thus far, I've identified parameters for symmetrical dimethylated ARG (sDMA)...

how to plot svg files from out file ( barnaba SEC_STRUCTURE Command )

1

Could you please instruct me how to plot svg files from out files that generated from barnaba ANNOTATE command ?

Database Visualization and Variation Inquiry

1

Thank you for creating this valuable tool. I'm wondering how I can visualize the database I've created following the documentation. Also, could you please summarize the variations I can expect...

ERROR: syntax error in file "parameters", line number 15733: syntax error in CHARMM nbfix

1

i am getting following error while running the equilibration phase please suggest the fix this error. ``` # # ACEMD version 3.7.3 # # Copyright (C) 2017-2024 Acellera (www.acellera.com) #...