VMD-L Mailing List

From: Gurunath Katagi (gurunath.katagi_at_gmail.com)
Date: Wed Apr 09 2014 - 01:18:35 CDT

Dear all,
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
minimization.

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

thank you
Gurunath