VMD-L Mailing List

From: Neeraj Agrawal (neer1980_at_gmail.com)
Date: Mon Jan 30 2017 - 11:29:19 CST

Hello,

I am using the following set of commands to generate a .psf and .pdb file
of the solvated & ionized protein:

package require psfgen
topology top_all36_prot.rtf
....
....
....
package require solvate
topology top_all36_prot.rtf
topology toppar_water_ions.str
solvate prot.psf prot.pdb -t 12 -o solvate

package require autoionize
topology top_all36_prot.rtf
topology toppar_water_ions.str
autoionize -psf solvate.psf -pdb solvate.pdb -neutralize

However, in the output, ionized.psf, I see the following lines:
REMARKS topology 0.top_all36_prot.rtf
REMARKS topology 2.top_water_ions.rtf
REMARKS topology /usr/local/lib/vmd/plugins/noarch/tcl/solvate1.6/wat.top
REMARKS topology /usr/local/lib/vmd/plugins/noarch/tcl/readcharmmtop1.1/
top_all27_prot_lipid_na.inp

I assume that topology files between charmm27 and charmm36 are identical
for proteins, water and common ions (Na+, Cl-). If not, how do I disable
the charmm27 topology files from the solvate and autoionize packages?

Thanks,
Raj