Problem with topology file

From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Sat Dec 18 2010 - 07:35:25 CST

Hi all,
I am trying to build a topology file for a GLUP to GLU FEP mutation,
but I get a fatal error involving atoms moving too fast.
This is symptomatic of atom clashes, hence wrong topology

Would anyone be really kind and have a brief look at my topology
I would appreciate it dearly!

GLUP (protonated, glumatic acid) is CG, HG1, HG2, CD, OE1, OE2, HE2

GLU (glutamate) is CM, HM1, HM2, CM2, OM1, OM2, HM2

! Mutate topology Glu-GluP

RESI MUT -1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HM1 OM1
ATOM HA HB 0.09 ! | | | //
GROUP ! HA-CA--CB--CM--CM2
ATOM CB CT2 -0.18 ! | | | \
ATOM HB1 HA 0.09 ! | HB2 HM2 OM2(-)
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CM CT2 -0.28
ATOM HM1 HA 0.09
ATOM HM2 HA 0.09
ATOM CM2 CC 0.62
ATOM OM1 OC -0.76
ATOM OM2 OC -0.76
GROUP
ATOM C C 0.51
ATOM O O -0.51
GROUP
CG, CATOM 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 CB CA CM CB CM2 CM OM2 CM2
BOND N HN N CA C CA
BOND C +N CA HA CB HB1 CB HB2 CM HM1
BOND CM HM2
BOND CD CG OE2 CD
BOND CG HG1
BOND CG HG2
BOND OE2 HE2
CMAP -C N CA C N CA C +N
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 CM 1.4512 111.0400 180.0000 115.6900 1.5557
IC CM CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145
IC CM CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131
IC CA CB CM CM2 1.5516 115.6900 180.0000 115.7300 1.5307
IC CM2 CB *CM HM1 1.5307 115.7300 117.3800 109.5000 1.1053
IC CM2 CB *CM HM2 1.5307 115.7300 -121.9600 111.0000 1.1081
IC CB CM CM2 OM1 1.5557 115.7300 180.0000 114.9900 1.2590
IC OM1 CM *CM2 OM2 1.2590 114.9900 -179.1000 120.0800 1.2532
IC HM2 OM2 CM2 OM1 0.0000 0.0000 0.0000 0.0000 0.0000
IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532
IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000
END

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