From: Prof. Eddie (
Date: Tue May 28 2013 - 14:43:16 CDT

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
    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?

Edward Ackad, Ph.D <>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390