Discussion around computational chemistry and cheminformatics tools for the Galaxy platform
- https://cheminformatics.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fchembl%2Fchembl%2F0.10.1%2Bgalaxy2
- https://cheminformatics.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fautodock_vina_prepare_receptor%2Fprepare_receptor%2F1.5.7%2Bgalaxy0
- https://cheminformatics.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fautodock_vina_prepare_box%2Fprepare_box%2F2020.03.4%2Bgalaxy0
I performed protein RNA complex simulation in Schrodinger, and want to study DCC for the same.
I covert Schrodinger trajectories to the DCC in VMD. I uploaded the pdb files and DCD file and was able to generate the graph for C-alpha atoms for protein.
for nucleic acid i was facing problem as i have tottle 48 nucleotide but DCC graphs was showing 1522 resides,which is due to atoms selection. i rectify that error using selecting the Atom id 'P'. which generated the graph for only 48 residues which i want.
Now the last step which i want is combine graph of protein and RNA residues, I have tabular file for booth as a different but i want combine graph for protein. I tried using CA and P for nucleic acid., but end up getting error.
It will be great help to generate the combine graph for protein and RNA.
trj <- read.dcd(trtfile, cell = FALSE)
NATOM = 30378
NFRAME= 1002
ISTART= 0
last = 1002
nstep = 1002
nfile = 1002
NSAVE = 1
NDEGF = 0
version 24
|======================== | 21%Error in readBin(trj, "numeric", size = 8, n = (a/8), endian = head$end) :
invalid 'n' argument
In addition: Warning messages:
1: In readBin(trj, "integer", 1, endian = head$end) :
closing unused connection 3 (wt.dcd)
2: In rbind(x, y, z) :
number of columns of result is not a multiple of vector length (arg 3) this is warning in reading pdb file.
Hi, I have a question regarding tool Remove counterions and fragments in chemicaltoolbox. When I use SMILES as an input, it seems to work fine but when I input InChI nothing happens.
Original InChI
InChI=1S/C13H14N4O3S.Na/c1-8-6-13(12(15)7-11(8)14)17-16-9-2-4-10(5-3-9)21(18,19)20;/h2-7H,14-15H2,1H3,(H,18,19,20);/q;+1/p-1
InChI after removing counterions and fragments
InChI=1S/C13H14N4O3S.Na/c1-8-6-13(12(15)7-11(8)14)17-16-9-2-4-10(5-3-9)21(18,19)20;/h2-7H,14-15H2,1H3,(H,18,19,20);/q;+1/p-1
grep but why write something if there is already such a tool :)
