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Questions related from Daniel Alpízar
Hello all, I have molecular dynamic simulations of three membrane-peptide systems, and I want to calculate the free binding energy of the peptide to each membrane. Which method is more accurate...
25 September 2023 1,711 2 View
Hello everybody, I am conducting a study to identify selected positive sites in a group of proteins using the Branch-site model implemented in Codeml-PAML. When I compare the null model to the...
15 February 2023 9,334 0 View
Hello I would like to know if somebody has a document that describe all patch that can be used in the vmd pluging PSFGEN or if there are any command line in the tk console that I could use to...
20 October 2021 4,356 2 View
Hello everybody, I am trying to download the top2psf.pl script from the VMD script library (https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/) but I am getting an error from...
20 July 2021 4,886 3 View
Dear all: I want to perform a coarse grain molecular dynamics simulations (by first time) using namd2, but I can't found the topology files needed to do it. I tried in the home page of MARTINI...
15 June 2020 2,078 2 View
Hello everybody: I´m trying to performance a blind docking in Swissdock but when I upload de ligand in .mol2 saved whit Chimera, this show me a problem, and told me that check its topology I take...
15 November 2017 4,293 6 View
I am doing the geometrical optimization of two isomers using a restrictive method. When I enter the command to the Gaussian software the output file show that one of the isomers always is...
01 January 1970 6,909 7 View
