making dipeptides with psfgen - CMAP terms?

From: Brian Radak (
Date: Tue Feb 17 2015 - 09:42:59 CST

I am making various dipeptides with psfgen, but I also compared the
analogous procedure with CHARMM.

However, when I check the gas phase energy of the compound, I get a
discrepancy in the dihedral energy corresponding to a missing CMAP term in
the PSF generated by psfgen (this is obvious when you set "mergeCrossterms

It looks like this is a tricky case, as the C36 files have special patches
just for dipeptides (at least a special ACED patch as opposed to the normal
ACE patch). There does not appear to be special CT3 patch for dipeptides
(should there be?). Is this something that psfgen was designed to do?

You can see this all in one namd configure file provided you adjust some
paths below:

load VMD_INSTALL_LIB_DIR/vmd/plugins/LINUXAMD64/tcl/psfgen1.6/

paratypeCharmm on
mergeCrossterms no
topology PATH_TO_CHARMM_PARAMETERS/toppar/top_all36_prot.rtf
parameters PATH_TO_CHARMM_PARAMETERS/toppar/par_all36_prot.prm

segment PROT {
  residue 1 ASP
  first ACED
  last CT3
  auto angles dihedrals
# need this to seed the IC table
coord PROT 1 N {0.0 0.0 0.0}
coord PROT 1 CA {1.48 0.0 0.0}
coord PROT 1 C {1.99 1.4 0.0}
regenerate angles dihedrals

set basename foo
writepsf ${basename}.psf
writepdb ${basename}.pdb

exclude scaled1-4
switching off
cutoff 999
outputname $basename
structure ${basename}.psf
coordinates ${basename}.pdb
temperature 0

run 0

Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812

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