07 July 2017 2 9K Report

Are there anyone who have experience on installing Matpack, C++ Numerics and Graphics Library ? I want to use this program to plot my data obtained from Gridmat-MD, for lipid bilayer analysis. I have attached here with the Makefile.common file. But, I don't know why I am running through errors when I use make install command. The error goes like this:

Makefile:79: /Makefile.version: No such file or directory

Makefile:87: /Makefile.common: No such file or directory

make: *** No rule to make target '/Makefile.common'. Stop.

My system is 64 bit Ubuntu. I would be very grateful if anyone could suggest me the edits that I have to make on my Makefile.common file for its installation.

Thanks

More Roshan Shrestha's questions See All
Gaps/Voids seen in POPC bilayer during MD simulation ?

Hi all, I am working on a MD simulation of a membrane protein inside the POPC bilayer using namd. At first, I ran a short constrained dynamics by applying harmonic constraints to both...

05 June 2019 7,291 4 View

Check if the lysine residues are deprotonated or not inside the membrane ?

Hi everyone, My system is a dimer. During the MD simulation, I can see a strong hydrogen bond formed between two lysine residues which are at the side chains of two peptides. But, the issue is...

04 May 2019 5,965 5 View

PDB manipulation options in Charmm GUI?

Hi everyone, While using the PDB reader of charmm-gui for my membrane protein system which is a dimer, I got stuck at PDB manipulation option. It gives me option regarding...

04 May 2019 2,169 3 View

Protein-lipid interaction ?

Can anyone please suggest me review articles/papers/books/links on understanding protein-lipid interactions through Molecular Dynamics simulation ? Thanks

01 February 2018 4,797 3 View

Definitive non-bonded distance to form a contact ?

Is there any standard value like two non-bonded residues or atoms are considered to form a contact if their distance is less than ? I usually use like 1.4 nm for short range non-bonded LJ cut-off...

01 February 2018 9,699 4 View

Plotting running average in python similar to in Xmgrace ?

Are there any scripts or tools available in python to plot the running average of the data similar to as shown in the figure attached? Thanks

31 December 2017 2,318 4 View

Rotate a specific residue and save the coordinates in VMD ?

I want to rotate a specific residue (say "resid 7 and resname MET") by 180 degrees around x-axis and save the coordinates. Can it be done using VMD's TK Console ?

31 December 2017 7,382 7 View

Thermal vibration of bonds ?

The characteristic frequency of thermal motion is around 7E12 Hz at room temperature (300K), but from that information how can we conclude that the bonds are hard; they don't vibrate !!

31 December 2017 5,947 2 View

Measurement of helical tilt (dimer tilt) using gmx helixorient ?

I want to measure the tilt of helix with the normal of bilayer. My system is basically a dimer with two helices. Since using sidechain atom relative to the axis is optional, I simply defined...

31 December 2017 457 3 View

Gromacs tool or any tools to look for the number of protein-lipid contacts ?

Are there any gromacs or other tools available to look for or find the number of protein-lipid contacts during Molecular Dynamics simulation of membrane protein ?

11 December 2017 2,664 3 View

Similar questions and discussions
Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

I got 02 moderator values defining Johnson-Neyman significance regions. Is it an error?

Hi everyone, I am conducting research for my Master's thesis. I am using PROCESS by Johnson-Neyman to analyze my Moderator model. I test the relationship between Public Service Motivation and...

03 March 2021 2,350 2 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

Do I need to strip the PVDF membrane before staining it with colloidal gold?

Dear Colleagues, After running Western blot on PVDF membrane and detection using ECL, I would like to stain my PVDF with colloidal gold to be able to allign the ECL image with total proteins on...

02 March 2021 7,829 3 View

PACYC PCR not working after several attempts. Would anyone have any suggestions?

So, I have been trying to run a pACYC PCR which will be used later on for a Gibson Assembly. However the PCR is not working. I have already tried gradient PCR and changing extension time; however...

02 March 2021 1,146 2 View

What SPSS analysis should I run with one IV (with two levels) and two DVs?

Hi, I am trying to figure out which test would be most appropriate to run for the following question: Is there a difference in task blood pressure between smokers and non-smokers? There are two...

01 March 2021 8,235 2 View

How can I integrate a routing protocol in a tiny device (e.g. Raspberry Pi)?

Hi Community, I'm facing the issue of integration/compiling a new routing protocol in a WSN simulator. The final goal is to successfully add, configure this routing protocol in hardware devices...

01 March 2021 9,332 6 View

OpenBCI eeg--has anyone used them?

I'm looking to try out an off-the-shelf EEG set for some exploratory work. Curious if anyone has used the OpenBCI, and how much set-up work is required. I've heard they are more difficult to get...

01 March 2021 4,128 3 View

Our partners will collect data and use cookies for ad personalization and measurement. Learn how we and our ad partner Google, collect and use data. Agree & close