VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Jan 30 2017 - 13:49:16 CST

Hi Raj,

That’s funny. I’ve never noticed that text in the remarks before. CHARMM 36 and CHARMM 27 differ slightly in their atomtypes. One of the easiest ones to check are the atomtypes on glutamate. In CHARMM 27, the CB atom has the CT2 type, but it has the CT2A type in CHARMM 36 (the sidechain hydrogens also have slightly different atomtypes, HA vs HA2). If you compare against these differences, you should see that psfgen did use the CHARMM36 style like you expected, since psfgen won’t replace residue definitions once they have been read in, and the CHARMM36 versions were read in first. The danger here is that if you forget to add in a needed component yourself (maybe for lipids around the protein?), psfgen will find the CHARMM27 version that got read in, which would result in mixing the two parameter sets together without you intending to.

Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>

On Jan 30, 2017, at 10:29 AM, Neeraj Agrawal <neer1980_at_gmail.com<mailto:neer1980_at_gmail.com>> wrote:

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