VMD-L Mailing List

From: Gurunath Katagi (gurunath.katagi_at_gmail.com)
Date: Wed Jan 01 2014 - 04:08:07 CST

Hi.
i have done the tutorial on Residue bases coarse grained simulation on
ubiquitin (06-otherExamples) and was trying to get the all atom
representation from the lastframe of coarsegrained simulation using CGtools
on vmd 1.9.1 using tcl scripting ..

# load the last frame of cg-protein without solvent
mol load pdb cg-lastframe-prot.pdb
mol addfile cg-ubiquitin-fixed.psf

# load the all-atom strcuture
mol load pdb AA-ubiquitin.pdb
mol addfile AA-ubiquitin.psf

package require cgtools
::cgtools::apply_reversal 0 cg-ubiquitin.rcg 1 rev-ubq.pdb 1
::cgtools::make_anneal_config rev-ubq.pdb AA-ubiquitin.psf
/home/gurunath/Downloads/c32b1/toppar/par_all27_prot_lipid.prm
rev-ubq-AA.namd no

>From here, the structure seems to be generated properly.

Just wanted to know whether one should solvate this molecule while using
the generated conf file for minimization and md ? Since in the conf file,
its applying a constraint on the atoms to maintain the cg, does the
addition of solvent affects the run ?

Thank you

Gurunath

  please let me know if there are any corrections or su