Re: making dipeptides with psfgen - CMAP terms?

From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Tue Feb 17 2015 - 16:10:49 CST

Great! That will save me a lot of trouble with re-doing my workflow to
include CHARMM. I'll test this with the new source and respond back if
anything looks amiss.

Brian

On 02/17/2015 01:53 PM, Jim Phillips wrote:
> Hi Brian,
>
> This is RESI ASP from the topology file:
>
> BOND CB CA CG CB OD2 CG
> BOND N HN N CA C CA C +N
> BOND CA HA CB HB1 CB HB2
> DOUBLE O C CG OD1
> IMPR N -C CA HN C CA +N O
> IMPR CG CB OD2 OD1
> CMAP -C N CA C N CA C +N
>
> You'll note that the items being skipped are those with -C or +N
> because there is no previous or later patch. The CMAP you want should
> be added by the ACED patch, but it requires that the CT3 patch also be
> applied to create the NT atom. The logic in psfgen applies ACED, then
> CT3.
>
> Actually, psfgen doesn't appear to do anything with cross-terms in
> patches because it's missing those lines, which would cause ACE, ACED,
> ACP, ACPD, and CT3 termini to be missing cross-terms. This was an
> easy fix, and I have also reversed the order to apply last (CT3)
> before first (ACED).
>
> The fix will be in the Feb 18 NAMD nightly build standalone psfgen.
> Please let me know if that does or does not resolve your problem.
>
> Thank you very much for catching and reporting this!
>
> Jim
>
>
> On Tue, 17 Feb 2015, Brian Radak wrote:
>
>> 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
>>

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

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