From: Neeraj Agrawal (neer1980_at_gmail.com)
Date: Mon Jan 30 2017 - 14:14:28 CST

Thanks Josh. I checked the psf file and indeed it has the correct CT2A atom
for the Glu residue. However, as you said, in some particular cases, psfgen
might borrow atomtypes from CHARMM27 topology file.

Is there any option to disable the "default" topology files in the psfgen,
solvate and autoionize commands so that these program use only the
user-specified topology files.

Thanks,
Raj

On Mon, Jan 30, 2017 at 11:49 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> 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
>
>