Urszula Sylwia Uciechowska-Kaczmarzyk

10 Questions 17 Answers 0 Followers

Questions related from Urszula Sylwia Uciechowska-Kaczmarzyk

Does anyone have an example input file for nvt and npt MD simulation with NAMD?

I follwed the NAMD tutorials for ssb and 1UBQ. I generated the structures using psfgen and run energy minimization. Thanks a lot for any help I am new to NAMD.

16 July 2015 426 5 View

How do I prepapre DNA for NAMD simulations?

Is there any fast way to change the DC on CYT for NAMD?

23 January 2015 5,715 2 View

How can I determine the Hbond occupancy with GROMACS?

Dear Gromacs users, I would like to run H-bond analysis in order to get a percentage H-bond occupancy between protein and DNA. How can I do it? I used the g_bond command but the obtained plot does...

30 October 2014 6,006 13 View

With regards to Gromacs Radius of gyration, how do I analyse the data?

Does anyone know how to analyse the plot obtained from gyration? I know what it means but I'm not sure how to use this measure or interpret data? I run MD for a protein in complex with DNA.

22 October 2014 9,374 1 View

Is it possible to run RMSD calculations in GROMACS?

Is it possible to run RMSD calculations for the part of the protein for example rmsd for AA 45-187? How to specify it using g_rms command?

16 October 2014 1,254 5 View

How do you calculate a hydrogen bond analysis between a residue and DNA in GROMACS?

How should I specify it after running make_ndx? for example r259 and DA2(from DNA). Does anyone know?

10 October 2014 3,735 3 View

Is there any (quick) tool to find a pentapeptide motif QL[SD]LF in common protein databases?

Representatives of this motifs are present in most sequenced members of the eubacterial, UmuC families and the MutS1. I found a paper from 2001 and would like to update the information (they used...

07 August 2014 2,091 1 View

Can anyone help me with homology modelling?

My protein system is missing about 40 amino-acids on the N-terminal. What is the best solution in this case? Run Modeller or I-Tasser and add the missing part to the protein? Would be possible to...

18 July 2014 8,777 8 View

How does one extend the protein simulation in Gromacs and check the total time of the MD?

I run MD simulations in GROMACS for 20ns which is 1000000 nsteps using dt= 0.02. I would like to extend it to another 20ns in order to have a complete run for 40ns. How should I proceed? According...

10 July 2014 9,806 25 View

Warning: pressure scaling more than 1% -GROMACS. Can anyone help?

I am working with gromacs and I have got a warning as shown below. Can you please suggest what to do to run my file completely. Please reply as soon as possible. I am awaiting your...

23 June 2014 10,683 9 View