Re: psfgen and charmm19: is there any inconsistency?

From: Mikolai Fajer (mfajer_at_gmail.com)
Date: Wed Jun 28 2006 - 14:06:43 CDT

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-

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