From: Jiawei Xu (
Date: Tue May 28 2013 - 15:45:46 CDT

Hi, Edward,

First, par_all_36_prot.prm is not a topology file but a parameter file.

Second, if it is a typo error,
It seems that your pdb file has some atom/molecule type not included in the
top_all36_prot.rtf topology file.

Third, par_all27_prot_lipid_na.inp included prot, lipid, and na. Thus you
can add all top_all36_prot.rtf, top_all36_lipid.rtf, and top_all36_na.rtf
files to PSF gen.

Good luck,

On Tue, May 28, 2013 at 3:43 PM, Prof. Eddie <> wrote:

> Hi all,
> I'm trying to combine a protein with a drug (ligand). I built a psf for
> the drug (by analogy using charm36_cgenff), merged the two and ran it in
> namd2 as a test. The protein had orginally been parameterized with autopsf
> using vmd's par_all27_prot_lipid_na.inp
> Since my ligand and protein were parameterized by different versions of
> the force field (charmm36 for the ligand and charmm27 for the protein) I
> thought my next step (aside from optimization of the ligand using fftk) is
> to reparameterized my protein with charmm36.
> Here I run into a few problems using the package from Mackerell's website (
> If I load the
> topology file par_all_36_prot.prm, delete the ligand chain autopsf will
> generate a error message with no useful info I can gather when I try to
> deprotinate a cystine:
> MOLECULE MISSING! Use resetpsf to start over.
> MOLECULE MISSING! Use resetpsf to start over.
> while executing
> "patch CYSD P1:97"
> ("eval" body line 1)
> invoked from within
> "eval "patch [lindex $patch 0] [lindex $patch 1]:[lindex $patch 2]""
> (procedure "::autopsf::makepatches_gui" line 17)
> invoked from within
> "::autopsf::makepatches_gui"
> invoked from within
> ".autopsf.patches.finish invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .autopsf.patches.finish"
> (command bound to event)
> If I include the topology file par_all27_prot_lipid_na.inp then
> it succeeds but I assume this means it just parameterized using charmm27
> not 36 as I want/need. Is there something I am doing incorrectly?
> Thanks,
> Eddie
> _________________________________________________________
> Edward Ackad, Ph.D <>
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390

Jiawei Xu