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Answers 6
Similar questions
Research that mentions Amber



Question
Asked 8 April 2020
Dhruvi Shah
 * Indian Institute of Advanced Research





HOW TO INSTALL AMBER TOOLS IN UBUNTU?

I have downloaded the AmberTools19 package but I am having issues in installing
it. I have tried to install using Installation guidelines in the Amber Tools pdf
but still no luck. Is it because GROMACS is already installed?
I would request if some one give me the details of installing AmberTools or any
other option from where I can use AmberGAFF for my ligand simulations?
Amber
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MOST RECENT ANSWER

Mehdi Irani
University of Kurdistan
Follow the instructions on the following webpage to install AMBER on Ubuntu. In
my research group, we developed the instructions based on our experience.

https://prof.uok.ac.ir/m.irani/index_files/Page312.htm

Following the instructions, you can install AmberTools21 on Ubuntu 18.04.6 LTS.
However, it might work with other versions of Amber Tools and UBUNTU.
Cite


POPULAR ANSWERS (1)

http://ambermd.org/Installation.php
Follow the exact procedure then go to bash and source.
Cite
4 Recommendations


TOP CONTRIBUTORS TO DISCUSSIONS IN THIS FIELD

Justin Lemkul
 * Virginia Tech (Virginia Polytechnic Institute and State University)



Michal H. Kolář
 * University of Chemistry and Technology, Prague



Dmitri Kireev
 * University of Missouri



Martin Klvana


Pedro L. Contreras E.
 * University of the Andes (Venezuela)






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ALL ANSWERS (6)

http://ambermd.org/Installation.php
Follow the exact procedure then go to bash and source.
Cite
4 Recommendations
Alex Rayevsky
National Academy of Sciences of Ukraine
Hi. After installation of Conda or miniconda (it seems to be more suitable for
the case) I used commands from the amber tools installamtion manual:
conda install ambertools=19 -c ambermd
conda install numpy
Then You have to reboot the system or maybe just re-enter the terminal window.
Now it works fine for me, there were no problems with dependences and so on...
In addition, GROMACS was already installed
Cite
2 Recommendations
Dhruvi Shah
Indian Institute of Advanced Research
Thank you all.

I am trying to install AmberTools19 and during installation I got this error-
Import Error: No module named setuptools
Makefile:505: recipe for target 'pytraj' failed
make[2]: *** [pytraj] Error 1
make[2]: Leaving directory  ' /mnt/c/Users/Hp/amber18/AmberTools/src'
Makefile:26: recipe for target 'serial' failed
make[1]: *** [serial] Error 2
make [1]: Leaving directory ' /mnt/c/Users/Hp/amber18/AmberTools/src'
Makefile: 7: recipe for target 'install' failed
make: *** [install] Error 2
Please help me
Cite
Dhruvi Shah
AmberTools19 installation explained by Alex Rayevsky is the best secure way to
install on any linux.

Cite
1 Recommendation
Mehdi Irani
University of Kurdistan
Follow the instructions on the following webpage to install AMBER on Ubuntu. In
my research group, we developed the instructions based on our experience.

https://prof.uok.ac.ir/m.irani/index_files/Page312.htm

Following the instructions, you can install AmberTools21 on Ubuntu 18.04.6 LTS.
However, it might work with other versions of Amber Tools and UBUNTU.
Cite



SIMILAR QUESTIONS AND DISCUSSIONS

How to restart simulation in Gromacs?
Question
9 answers
 * Asked 14 November 2020

 * Nadim Ferdous

I tried to run a 500ns MD simulation of a protein in Gromacs. Due to power
failure, my pc turned of after around 450+ ns. Now I want to restart the
simulation from that point. I used the following command-"gmx mdrun -v -deffnm
md_0_1 -cpi md_0_1.cpt -append", but found that I dont have any cpt file. Now
how should I do this? Is there any other way? If not, then how to generate the
cpt file of my simulation?
View
How to use pbc wrap command in vmd to re-center a multimeric protein?
Question
27 answers
 * Asked 19 February 2016

 * Tugba Ozturk

During MD simulation, tetrameric protein diffuses in the simulation box and ends
up crossing the periodic boundaries. One of four chains is jumping to the other
side of the simulation box. For my analysis, I need all chains together and
centered. 
I tried to use pbc wrap in VMD. But after wrapping the trajectory file, some of
atoms are being transformed in an awkward way so I end up seeing stretches while
visualizing the protein in new cartoons mode. I am guessing it's because of
center of mass of my selection moving significantly. 
The command I have used:
pbc wrap -center com -centersel "protein" -compound residue -all
I could not find a way to fix that, somebody else reported a similar problem in
vmd mailing list, so far no replies.
Any suggestions?
View
How to generate secondary structure trajectory plot from "dat" file?
Question
17 answers
 * Asked 14 May 2023

 * Ankur Chaudhuri

Could you please help me to sort out one Gromacs problem?
When I run gmx dssp (Gromacs 2023) command, it generates .dat file (e.g. ss.dat)
as output. (.xpm is not working in Gromacs 2023). How do I generate the of plot
trajectory of secondary structure by using .dat file? I have attached the .dat
format.

View
How can I simulate a metalloprotein-ligand complex in GROMACS?
Question
3 answers
 * Asked 26 April 2023

 * Marwa Abd El Kader Zaater

I was wondering what changes should I add in the MDS protocol to account for the
Zn ion in the active site of a metalloprotein.
Also, I would be grateful if there was a bash script available to automate the
process.
View
How to perform MMPBSA using Gromacs ??
Question
8 answers
 * Asked 12 October 2020

 * Rik Ganguly

Can anyone suggest me the proper way to perform MMPBSA using Gromacs ??
View
Does anyone have access for PRODRG server?
Discussion
2 replies
 * Asked 7 March 2023

 * Sukumar Ranjith

Need a download link
View
How to convert Gromacs files to Amber output files?
Question
2 answers
 * Asked 26 February 2023

 * Ekrem Yaşar

I want to use cpptraj for some analysis but I need to convert my topology and
trajectory files from Gromacs xtc, tpr format to Amber nc and parm formats.
Could you please let me know how can I convert topology and trajectory files
from Gromacs to Amber?
View
How Shall I perform Principle Component Analysis in GROMACS?
Question
8 answers
 * Asked 14 December 2020

 * Debanjan Kundu

I have to perform PCA as a part of my results and analysis of protein-ligand
complex docking using GROMACS 2018.8. How shall I perform PCA and interpret the
results for the same?
Any insights will be highly appreciated.
View
How to install ACPYPER and ANTEAMBER software in Linux?
Question
7 answers
 * Asked 17 December 2018

 * Sourav Pal

I want to do GROMACS simulation using ffamber_99sb forcefield. so that i have to
generate the topology of the small molecules by ACPYPE. So can you tell me how
to install ACPYPE and Anteamber installation together? Thanks in Advance.
View


RELATED PUBLICATIONS

The Origin of Insect-Borne Human Diseases as Revealed in Amber
Article
Full-text available
 * Jul 2011

 * George Poinar


View
AMBER: Assisted model molecules and their interactions
Article
 * Jan 1981

 * Paul Weiner
 * P.A. Kollman


View
New cantacaderid lace bugs from Dominicam Amber
Article
Full-text available

 * Yuri Popov
 * V. B. Golub


View
Got a technical question?
Get high-quality answers from experts.
Ask a question


TOP CONTRIBUTORS TO DISCUSSIONS IN THIS FIELD

Justin Lemkul
 * Virginia Tech (Virginia Polytechnic Institute and State University)



Michal H. Kolář
 * University of Chemistry and Technology, Prague



Dmitri Kireev
 * University of Missouri



Martin Klvana


Pedro L. Contreras E.
 * University of the Andes (Venezuela)



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