From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Jan 21 2015 - 01:37:05 CST
This can be made a lot less arduous with a couple of simple modifications to autopsf (found in {vmd directory}/plugins/{architecture}/tcl/autopsf1.4).
In the pkgIndex.tcl file in that directory, change the line that starts "package ifneeded autopsf" to
package ifneeded autopsf 1.4 "source [list [file join $dir autopsf.tcl]] ; set env(AUTOPSFDIR) [list $dir]; set env(CHARMMFFDIR) /path/to/CHARMM-36"
(changing the bit at the end to the path where your CHARMM-36 parameter files are found). Then, in autopsf.tcl, search for "lappend topfiles" (should be around line 257), and replace those lines with:
lappend topfiles [file join $env(CHARMMFFDIR) top_all36_prot.rtf]
lappend topfiles [file join $env(CHARMMFFDIR) top_all36_lipid.rtf]
lappend topfiles [file join $env(CHARMMFFDIR) top_all36_na.rtf]
lappend topfiles [file join $env(CHARMMFFDIR) top_all36_carb.rtf]
lappend topfiles [file join $env(CHARMMFFDIR) top_all36_cgenff.rtf]
lappend topfiles [file join $env(CHARMMFFDIR) top_all36_prot.rtf]
lappend topfiles [file join $env(CHARMMFFDIR) stream/toppar_all36_carb_glycopeptide.str]
lappend topfiles [file join $env(CHARMMFFDIR) toppar_water_ions.str]
You may need to add a few others depending on the systems you tend to work with, but that should cover most systems you're likely to encounter. Next time you start VMD you'll find these are pre-loaded in autopsf so you don't have to go through picking them every time. You will of course have to include all the necessary parameter files in your NAMD script as well. Just remember the rule that the stream files come last.
Cheers,
Tristan
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Branko <bdrakuli_at_chem.bg.ac.rs>
Sent: Monday, 19 January 2015 3:46 AM
To: namd-l_at_ks.uiuc.edu; Maria Bykhovskaia
Subject: Re: namd-l: using NAMD with CHARMM36 ff
Maria,
Try to add 'par_all36_carb.prm' among parameters. I suppose that you have no carbohydrates, but also you have no atoms from cgenff, and ff developers advised to add all prm files . 'toppar_water_ions_namd.str' usually performs well with NAMD. If problem persist, try to generate psf with CHARMM gui (http://www.charmm-gui.org/)
Branko
On 1/18/2015 2:26 AM, Maria Bykhovskaia wrote:
Hi,
I tried to use ChARMM36 force field, and I am getting the message:
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2
my system does not have the atom type OC2D2
It runs with Charmm27 without errors. The system includes a protein and membrane with water (TIP3) and ions (POT, CLA, CAL), psf was generated with VMD, and Charmm36 topology was used to build the lipid bilayer.
My input file looks this way:
paraTypeCharmm on
parameters par_all36_lipid.prm
parameters par_all36_prot.prm
parameters par_all36_cgenff.prm
parameters toppar_water_ions_namd.str
mergeCrossterms yes
Will appreciate any suggestions.
Thanks,
Maria
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