RE: regarding editing protonated glutamate in the pdb file via psfgen . .

From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Tue Nov 05 2013 - 01:38:20 CST

GLUP as defined here is a patch to create protonated glutamine from glutamine.

So, in your script generating the psf, you simply have to call this patch and apply it to residue 173

-Erik
________________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of Prathit Chatterjee [pc20apr_at_yahoo.co.in]
Sent: Tuesday, November 05, 2013 12:53 AM
To: NAMD Mailing list
Subject: namd-l: regarding editing protonated glutamate in the pdb file via psfgen . .

Dear NAMD-Experts,

I need an assistance regarding editing a pdb file containing a protonated Glutamate.

I am pasting below the description of Glutamate (Glu) and protonated Glutamate (GluP) given in topology.

GLUTAMATE

RESI GLU -1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 OE1
ATOM HA HB 0.09 ! | | | //
GROUP ! HA-CA--CB--CG--CD
ATOM CB CT2 -0.18 ! | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 OE2(-)
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.28
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
ATOM CD CC 0.62
ATOM OE1 OC -0.76
ATOM OE2 OC -0.76

............................. ............................. ...........

PROTONATED GLUTAMATE

PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2
GROUP ! via acetic acid, use in a patch statement and
                       ! follow with AUTOgenerate ANGLes DIHEdrals command
ATOM CG CT2 -0.21 !
ATOM HG1 HA 0.09 ! HG1 OE1
ATOM HG2 HA 0.09 ! | //
ATOM CD CD 0.75 ! -CG--CD
ATOM OE1 OB -0.55 ! | \
ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2
ATOM HE2 H 0.44 !
BOND OE2 HE2
DONOR HE2 OE2

............................ .............................. ...

In my pdb, Glu 173 is protonated.

So, while editing for creating psf and pdb files; I included the following line :

set G173 [atomselect top "resname GLU and resid 173"]
$G173 set resname GLUP

But, the psfgen is not recognizing the resname GLUP (inspite of the toplogies of Protonated Glutamate are given).

 So, I don't know how to edit this particular protonated Glutamate and make psfgen work for creating the pdb and psf.

Any assistance regarding this will be greatly appreciated.

Thanking You,

Prathit

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