network analysis with conserved water molecules

[santosh chaudhary]

Hi, I want to do network analysis by taking conserved water molecules in to consideration. I used vmd to identify conserved water molecules in the trajectory (Is there any way to do this in Bio3d?). I tried calculating node betweenness but it turned out to be zero for all waters (for dcut value 4.5-10). Any suggestion will be of great help.

thank you santosh

[Xinqiu Yao]

Hi,

Can you tell a little bit more details about how you constructed the network and calculated node betweenness? Are you sure the water molecules are within the network?

Bio3D doesn't find "conserved" water automatically, but if you have residue numbers for these water, it would be straightforward to find them in R with the atom.select() function.

[santosh chaudhary]

Hi Xin, The trajectory and pdb file containing conserved waters along with ligand molecules were saved using vmd. I used following set of commands to build network and node centrality.

inds_2_chA <- atom.select(pdb_2.1)
trj_1_chA <- fit.xyz(fixed = pdb_2.1$xyz, mobile = dcd_1.1,  fixed.inds = inds_2_chA$xyz, mobile.inds = inds_2_chA$xyz)
cij_1_chA <- dccm(trj_1_chA[, inds_2_chA$xyz], grpby=pdb_2.1$atom[inds_2_chA$atom, "resno"])
cm_1_chA <- cmap(trj_1_chA[, inds_2_chA$xyz], grpby=pdb_2.1$atom[inds_2_chA$atom, "resno"], dcut=4.5, scut=0, pcut=0.75, mask.lower=FALSE, ncore=8)
net.cut_1_chA <- cna(cij_1_chA, cutoff.cij=0.30, cm = cm_1_chA, ncore = 8)
node.betweenness_1_chA <- betweenness(net.cut_1_chA$network)

Below are the output of pdb and network summary.

pdb_2.1 Total Models#: 1 Total Atoms#: 1736, XYZs#: 5208 Chains#: 1 (values: X)

 Protein Atoms#: 1671  (residues/Calpha atoms#: 210)
 Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

 Non-protein/nucleic Atoms#: 65  (residues: 13)
 Non-protein/nucleic resid values: [ ATM (1), ATP (1), MG2 (1), WAT (10) ]

summary(net.cut_1_chA)

                                                  c(1:3, 122, 124, 200:210)
                                         c(4:7, 21, 24:38, 78:94, 123, 126)
                                     c(8, 10, 98:99, 125, 127:130, 171:175)

c(9, 11:20, 22:23, 95, 131:133, 141:143, 176:189, 212:214, 217, 219:220,223) c(39:42, 44:49, 51, 61:66, 69:70, 72:74, 76:77, 96:97, 100, 211, 215:216, 222) c(43, 50, 52:60, 144:148) c(67:68, 71, 75, 110:121, 218) c(101:109, 149:170) 134:140 190:199 221

so we can see some waters in the network only one water (221) is isolated and if we increase the cij cut off more waters get isolated but not all.

thanks & regards santosh

[Xinqiu Yao]

Hi,

Could you send me an example network along with pdb if you haven't found solutions by yourself? ([e-mail])

[santosh chaudhary]

Hi Xin-Qiu,

I have mailed network file alond with pdb file to the given mail id.

regards santosh

[Xinqiu Yao]

Okay, thanks. I will look into it and get you back shortly.

[Xinqiu Yao]

Has replied by E-mail. This is more a question related to network method than that of Bio3D.