Saves specifics frames from molecular dynamics

[JFaya]

Hi everyone, i want to saves specifics frames (for example: frames 10 to 20 or just one frame), from my molecular dynamics and with the write.pdb option is not enough.

Can you help me with that.

This is part of my script:

ca.inds <- atom.select(pdb,resno = c(1:231), elety="CA")

ca.inds1 <- atom.select(pdb, resno = c(34:70), elety = "CA")

xyz <- fit.xyz(fixed=pdb$xyz[1,], mobile=dcd, fixed.inds=ca.inds$xyz, mobile.inds=ca.inds$xyz)

Thanks a lot

[Barry Grant]

Just use the frames you want as the xyz row indices.

For example, if I want to output frame 10 and separately frames 12 to 15:

write.pdb(pdb, xyz=xyz[10,], file="myframe_10.pdb")

write.pdb(pdb, xyz=xyz[12:15,], file="myframe_12-15.pdb")

This assumes your pdb object matches your trajectory and xyz is the trajectory in the from you want (following on from your code above).