How can i install NAMD or CHARMM biomolecule software?

More I.O. Arukalam's questions See All

Please i need help on how to predict the future values with a trained Narx Neural Network.

I have successfully trained a dataset using Narx Neural Network. I am satisfied with the output of the Network. I want to use the network to predict unknown future values with inputs such as (1....

04 May 2017 470 0 View

I am having problem installing NAMD on my windows 7 computer. Please can someone give me idea on how to solve this problem?

I am trying to install NAMD on windows 7, but my computer keep showing "The program can't start because tcl85t.dll is missing from your computer. Try reinstalling the program to fix this problem"....

31 December 2016 2,014 1 View

How to obtain parameters to run a simulation for benzene using CHARMM forcefield in GROMACS?

I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...

15 February 2021 5,561 3 View

Can I use the CHARMM GUI input files for Gromacs in HPC?

Good day everyone! I am a Biochemistry undergraduate in the Philippines and to be very honest, we have no background in bioinformatics since we really focused on wet lab techniques + theory. Due...

15 February 2021 3,422 4 View

Charmm/GROMACS Residue 'ZN' not found in residue topology database?

I am trying to do some MD simulations of a protein with zinc ions. I am trying to use a charmm forcefield (I have tried 2017 and 2021) and Gromacs. I get an error when doing pdb2gmx Residue 'ZN'...

12 February 2021 9,367 2 View

Anyone use GROMACS' pdb2gmx for Adenosine monophosphate (AMP) to use with CHARMM force field?

I am trying to use the following command in GROMACS to generate a CHARMM topology file: gmx pdb2gmx -ff charmm27 -f amp.pdb -o amp.gro -p amp.top The atom list in my pdb file (amp.pdb)...

01 February 2021 7,769 6 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

31 January 2021 6,321 1 View

Does AMBER or CHARMM force field parameters have coarsed grained side chain parameters?

I need to coarse grain the side chain with a single atom. However, what force field parameters do I have to use. Does AMBER or CHARMM have any parameters and partial charges for coarse-grained...

31 January 2021 7,091 3 View

How to prepare an algal sample for FT-IR spectroscopy?

Can we measure the bulk composition of biomolecules present within an algal sample directly by placing its powdered form on a FT-IR spectroscopy stage? Or does it require a particular kind of...

30 January 2021 2,303 4 View

The lipid bilayer broken down and form micelle within 1ns MD simulation. How to simulate lipid bilayer without breaking bilayer?

To simulate the lipid bilayer (10-10, 25-25 so on) from CHARMM-GUI membrane builder, we used to simulate it at various force field (AMBER14, AMBER03, AMBER14IPQ, AMBER15FB, NOVA, YAMBER) at water...

26 January 2021 7,816 2 View

How to increase GPU usage during MD simulation?

The GPU usage percentage of my Nvidia Quadro K3100M does not exceed 10% during running MD simulation of protein of 252 residue length using VMD/NAMD software. Any one can provide advice on how...

08 January 2021 7,594 3 View

How to solve "Too many atoms in a patch" error?

Hi all, I was trying to run a simulation in NAMD but encountered the following error: FATAL ERROR: CudaTileListKernel::buildTileLists, maximum shared memory allocation exceeded. Too many atoms in...

01 January 2021 6,491 3 View

Martin Klvana

Do you have a problem with installing or running NAMD? If the latter: post the command you use to run NAMD and the error message you get from NAMD.

Setayesh Yasami

Hi,

There are similar discussions you might find useful:

1- http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/1873.html

2- https://www.researchgate.net/post/How_do_I_properly_install_NAMD_and_VMD_on_Windows_7

3-https://www.researchgate.net/post/Problem_running_64_bit_verson_of_NAMD_on_Windows7

anyway, I think Ubuntu is better for you. I hope it helps.

setayesh