how to do: FEP e2?, a protonating mutation?

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Tue Apr 07 2009 - 19:15:19 CDT

Dear All,

I am trying to write my own FEP mutation: GLU -> GLUP.

Attached you will find my first attempt (the "B" in "E2B" I defined for
"GLUP"). Is the logic for this right? (I don't expect you guys to look
for typos).

Is there a nice script doing these things in a breeze?

Cheers,
Sebastian

RESI E2B -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 CGA CT2 -0.28
ATOM HG1A HA 0.09
ATOM HG2A HA 0.09
ATOM CDA CC 0.62
ATOM OE1A OC -0.76
ATOM OE2A OC -0.76
GROUP ! via acetic acid, use in a patch statement
ATOM CGB CT2 -0.21 !
ATOM HG1B HA 0.09 ! HG1 OE1
ATOM HG2B HA 0.09 ! | //
ATOM CDB CD 0.75 ! -CG--CD
ATOM OE1B OB -0.55 ! | \
ATOM OE2B OH1 -0.61 ! HG2 OE2-HE2
ATOM HE2B H 0.44 !
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CGA CB CDA CGA OE2A CDA
BOND CB CA CGB CB CDB CGB OE2B CDB
BOND N HN N CA C CA
BOND C +N CA HA CB HB1 CB HB2 CGA HG1A
BOND C +N CA HA CB HB1 CB HB2 CGB HG1B
BOND CGA HG2A
BOND CGB HG2B
BOND OE2B HE2B
ANGLE HE2B OE2B CDB
DIHE HE2B OE2B CDB OE1B HE2B OE2B CDB CGB
DOUBLE O C CDA OE1A
DOUBLE O C CDB OE1B
IMPR N -C CA HN C CA +N O
!IMPR OE1A CGA OE2A CDA
!IMPR OE1B CGB OE2B CDB
IMPR CDA CGA OE2A OE1A
IMPR CDB CGB OE2B OE1B
DONOR HN N
DONOR HE2B OE2B
ACCEPTOR OE1A CDA
ACCEPTOR OE1B CDB
ACCEPTOR OE2A CDA
ACCEPTOR O C
IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961
IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216
IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501
IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306
IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530
IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516
IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828
IC N CA CB CGA 1.4512 111.0400 180.0000 115.6900 1.5557
IC N CA CB CGB 1.4512 111.0400 180.0000 115.6900 1.5557
IC CGA CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145
IC CGB CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145
IC CGA CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131
IC CGB CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131
IC CA CB CGA CDA 1.5516 115.6900 180.0000 115.7300 1.5307
IC CA CB CGB CDB 1.5516 115.6900 180.0000 115.7300 1.5307
IC CDA CB *CGA HG1A 1.5307 115.7300 117.3800 109.5000 1.1053
IC CDB CB *CGB HG1B 1.5307 115.7300 117.3800 109.5000 1.1053
IC CDA CB *CGA HG2A 1.5307 115.7300 -121.9600 111.0000 1.1081
IC CDB CB *CGB HG2B 1.5307 115.7300 -121.9600 111.0000 1.1081
IC CB CGA CDA OE1A 1.5557 115.7300 180.0000 114.9900 1.2590
IC CB CGB CDB OE1B 1.5557 115.7300 180.0000 114.9900 1.2590
IC OE1A CGA *CDA OE2A 1.2590 114.9900 -179.1000 120.0800 1.2532
IC OE1B CGB *CDB OE2B 1.2590 114.9900 -179.1000 120.0800 1.2532
IC HE2B OE2B CDB OE1B 0.0000 0.0000 0.0000 0.0000 0.0000

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