06 June 2015 4 3K Report

i am a newbie to gromacs(molecular dynamics software), please help me out. i compiled gromacs 5.0.2 for mac and successfully done installing it. But when i checked the following command mdrun -version it showed that gpu support is disabled. please help me out with this issue and guide me from basics.

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I want to test dihedral PCA for my mutated pocket and have trouble understanding the tutorial. How can i generate covar.ndx from the dihedral angles generated in before step. And regarding the...

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Mutation causing integer unperturbed charge of system. What to do?

The wild type protein has shown no integer charge where as a mutation in protein R175H has produced an integer charge in system. I used pymol to mutate. is it the centre of problem. Help wil be...

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How to renumber residue numbers in .gro and .top?

how can i renumber .gro and .top residue numbers to start with a specific number. The scenario is that i have first 40 residues of DNA and i dont want to disturb them. I just want to renumber from...

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How to perform cationic dummy atom model for a zinc contaning protein?

I am finding it difficult to perform cationic dummy atom model for p53 protein. can anyone suggest me a good and little detailed procedure. * if i perform it with xleap program of ambertools14,...

01 February 2016 2,946 0 View

[SOLVED]How to solve xleap error ( no leaprc in search path)?

I am getting an error in xleap module of Ambertools 14 in which it is unable to find leaprc nor anyother file i added to respective folders as said in this tutorial...

01 February 2016 7,368 2 View

How to get minimum energy structure from MD?

how can we decide on least energy structure of protein and ligand complex from MD simulation.

01 February 2016 5,285 1 View

Can youSuggest me best softwares for TEMPLATE DOCKING of ligands?

Molegro Virtual Docker is now little difficult to access and use so can any one please suggest better reliable software for template based LIGAND docking where a template of the ligand is made and...

09 October 2015 9,015 0 View

Why is measurefit in VMD showing following error "measure fit: selections must have the same number of atoms" ?

I tried to align molecules basically proteins at different frames to understand the ligand interaction. But to my dismay it shows an error "measure fit: selections must have the same number of...

08 September 2015 8,589 0 View

Is there a way to decrease gpu/cpu ratio of performance in GROMACS?

when ever i run a simulation in gromacs i end having a note saying GPU is 20% more in use than cpu which could decrease the performance and GPU/CPU ratio is 7.5 which should be ideally. Suggest me...

07 August 2015 2,557 0 View

How can I improve the GA341 score in the modelled protein in modeller?

I have performed series of modelling experiments using modeller to get a series of modeller proteins. But here i am unable to produce models with good GA341 score. I have a hundred percent match...

02 March 2015 6,043 9 View

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