Marlet Martínez-Archundia

5 Questions 12 Answers 0 Followers

Questions related from Marlet Martínez-Archundia

How could I run MD simulation of a cytochrome (including the heme group)?

Dear all, I am planning to run a MD of a cytochrome using the NAMD Program. I have checked that topology files of CHARMM27 such as: (top_alll27_prot_lipid.inp) which includes some lines about...

02 February 2019 1,985 4 View

How could I select a range of ATOMS by using VMD Program?

Dear all, I have been searching in the web and VMD Tutorials how to select a range of atoms by using VMD however I have just found only how to select a range of residues for example residue:...

09 September 2018 4,976 6 View

How to measure correctly the cell dimensions by using the measure minmax command in VMD?

Dear all, Recently, I have been running a MD simulation however I got the error "Periodic cell has became too small for orginal patch grid" and this mesagge could be related to the incorrect...

08 August 2018 6,825 5 View

How to wrap a protein correctly using VMD and save a new dcd?

Dear all, I have been trying to "wrap" my protein in the trajectory using the following command, using VMD: set sel [atomselect top protein] pbc wrap -centersel $sel origin -compound res -all. I...

04 April 2016 3,972 6 View

calculating the center of mass using Ptraj in Amber?

I am very interested to obtain center of mass of my protein subunits and the measure distance and angle between the atom groups. I wonder if anyone can explain to me how could I calculate the...

04 April 2014 1,544 6 View