Re: psfgen and charmm19: is there any inconsistency?

From: Elsa F. Sousa Henriques (Henriques_at_fias.uni-frankfurt.de)
Date: Thu Jun 29 2006 - 03:33:59 CDT

Hi,

If in the NAMD configuration file one uses <exclude scaled1-4> then
atom pairs matching the 1-4 criteria have their non-bonded interactions
included with the electrostatic term scaled by the 1-4scaling factor
and the vdW one modified by using the special 1-4 parameters defined in
the parameter files ... right?!.
If I remember it correctly, CHARMM19 explicit exclusions were ment for
some of these 1-4 interactions to be actually excluded, e.g., the one
between atoms CG and CZ in the PHE aromatic ring, and the NNB section
of the psf file was used for that (it was controlled by the NBXMod
keyword in the charmm program)...

Elsa

Quoting Mikolai Fajer <mfajer_at_gmail.com>:

> Hello Magali,
>
> I had a similar problem. PSFgen was written to support CHARMM27
> topology files, which are slightly different from CHARMM19. The
> explicit exclusions found in the CHARMM19 topology files are no longer
> supported in CHARMM, and thus in PSFgen. Fortunately, this problem
> can be easily fixed. Create a copy of the toph19.inp (say,
> toph19_psfgen.inp) and remove the explicit exclusions. The only
> explicit exclusions in toph19.inp occur in the residues you mentioned
> (PHE, TRP, TYR). I do not quite understand what the explicit
> exclusions do, but I have successfully used PSFgen and the modified
> toph19.inp to mutate proteins in the past.
>
> Following is an excerpt from our CHARMM19 topology file. Notice the
> fifth column on atoms CG, CD1, and CD2. These are the explicit
> exclusions. Simply delete those entries in the toph19_psfgen.inp and
> PSFgen should work just fine.
>
> RESI PHE 0.00000
> GROU
> ATOM N NH1 -0.35
> ATOM H H 0.25
> ATOM CA CH1E 0.10
> GROU
> ATOM CB CH2E 0.00
> ATOM CG C 0.00 CZ
> ATOM CD1 CR1E 0.00 CE2
> ATOM CD2 CR1E 0.00 CE1
>
> After modification it reads:
> RESI PHE 0.00000
> GROU
> ATOM N NH1 -0.35
> ATOM H H 0.25
> ATOM CA CH1E 0.10
> GROU
> ATOM CB CH2E 0.00
> ATOM CG C 0.00
> ATOM CD1 CR1E 0.00
> ATOM CD2 CR1E 0.00
>
> Let me know if this works for you.
>
> --
>
> -Mikolai Fajer-
>

-- 
Elsa Henriques, Ph.D.
Frankfurt Institute for Advanced Studies   Tel: +49 (0)69 798 47502
Max von Laue Str. 1, room 1.215            Fax: +49 (0)69 798 47611
60438 Frankfurt am Main, Germany        E-mail: 
Henriques_at_fias.uni-frankfurt.de
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