VMD-L Mailing List
From: Gurunath Katagi (gurunath.katagi_at_gmail.com)
Date: Wed Apr 09 2014 - 01:18:35 CDT
I am doing a simulation of protein which contains D-proline. I have
included the CHARMM topolgies for D-PRO (DPR) from Swisssidechain and have
obtained the .psf file. This psf along with pdb seems to correct after
However when solvate the protein using solvate plugin in vmd (1.9.1), I see
that PRO atoms seems to moved far (CA atom).
Can anyone point whats going wrong when i solvate the protein..
mol load psf prot1.psf pdb prot1.pdb
package require solvate
solvate prot1.psf prot1.pdb -t 10 -o prot1_wb