From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Tue Feb 17 2015 - 12:06:54 CST
Just a quick follow up, apparently this CMAP omission is intentional, as
evidenced by the error(?) messages:
psfgen) Info: skipping bond C-N at beginning of segment.
psfgen) Info: skipping improper C-CA-N-O at beginning of segment.
psfgen) Info: skipping improper N-C-CA-HN at beginning of segment.
*psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of
segment.*
psfgen) Info: skipping conformation CA-C-N-CA at beginning of segment.
psfgen) Info: skipping conformation N-CA-C-O at beginning of segment.
psfgen) Info: skipping conformation N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
(bold added by me). All of the other messages are apparently consistent
with CHARMM behavior. Again, I guess this is a confusing case because we
only have ONE residue and it is also the first/last residue. Any
suggestions?
Brian
On Tue, Feb 17, 2015 at 9:42 AM, Brian Radak <brian.radak.accts_at_gmail.com>
wrote:
> 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
> no").
>
> 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/libpsfgen.so
>
> 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
> guesscoord
>
> 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
> e-mail: radak_at_uchicago.edu
>
-- 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 e-mail: radak_at_uchicago.edu
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