Ma'mon M Hatmal

13 Questions 8 Answers 0 Followers

Questions related from Ma'mon M Hatmal

Please anyone to help in preparing qm/mm input files by "namd" (Molecular Dynamics software) for a ligand-enzyme complex?

Hi All, I'm trying to prepare qm/mm files for a ligand bound to an enzyme, I followed the tutorial of "vmd" and "namd", but it still reports an error in qm calculations. Any idea please? Best,

09 September 2018 869 0 View

Can anyone please help in finding the Fourier transform of the distance equation?

Can anyone please help in finding the Fourier transform of the distance equation? The distance equation is: (Z2-Z1)2+(Y2-Y1)2+(X2-X1)2=D2 X1,Y1,Z1 are the coordinates of the first point. X2,Y2,Z2...

05 May 2017 216 3 View

I need simple executable to perform steepest descent minimization for protein structure (pdb)?

Hi all, I need simple executable to perform steepest descent minimization for protein structure (pdb), with instruction how to do it? Thanks,

11 November 2016 7,788 1 View

How to Call NAMD Molecular dynamics software from *.bat file on windows?

Hi All, 1-How Can I call "NAMD" (Molecular Dynamics software) from *.bat file on windows. Usually, I use cmd.exe to run NAMD by the following command: namd2 +p12 input.conf > output.log. I...

10 October 2016 7,526 0 View

How I can apply random incremental pulse search (RIPS)?

Hi All, Can any one please tell me how I can apply "random incremental pulse search" (RIPS) for side chains of amino acids interacting with certain ligand. Which software (with link to the...

09 September 2016 1,786 0 View

Can anyone please explain if there is any software to produce coarse-grained 3D structure for RNA and DNA?

Can anyone please explain if there is any software to produce coarse-grained 3D structure for RNA and DNA?, I'm interested in the model of five key atomic positions in each nucleotide: two beads...

06 June 2016 3,368 5 View

Where can I find forcefields for phosphoserine to use with "NAMD"?

In Running MD simulations of some enzymes containing phosphoserine, where can we find forcefields for phosphoserine to use with "NAMD". Thanks,

06 June 2015 7,110 6 View

In Molecular dynamics, which ensemble is better to use: NVE or NVT?

We use different ensembles in MD, which one is preferred to use?

03 March 2015 7,389 14 View

In Molecular dynamics (NVE), is energy drift of about +5 Kcal/mol.ns acceptable?

In Molecular dynamics (NVE ensemble), is energy drift of about +5 Kcal/mol.ns acceptable?

03 March 2015 3,786 2 View

How can we solve the problem of energy drift in NVE ensemble in Molecular Dynamics?

How can we solve energy drift problem in NVE (constant energy, constant volume, and constant number of particles) ensemble in Molecular Dynamics?

03 March 2015 1,329 3 View

With NAMD, where can we find standard config files for minimization, heating, equilibration,and production for all types of ensembles (NVE,NVT,& NPT)?

With NAMD, Where can we find standard config files for minimization, heating, equilibration, and production for all types of ensembles (NVE,NVT,& NPT)?

03 March 2015 6,185 4 View

We have developed novel approaches for pharmacophore modeling based on Molecular dynamics and related methods , we can give online training

we have developed novel approaches for pharmacophore modeling based on Molecular dynamics and related methods , we can give online training.

01 January 1970 5,365 1 View

How to make a loop of two protocols in pipeline pilot, and how to pass the output from one to another?

Hi All, I'm trying to perform Molecular dynamics for a protein with a ligand for 100 steps, followed by qm/mm minimization for one step. I need to loop the two protocols 50 times, any help...

01 January 1970 341 1 View